@@ -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: 2023-02-27 Mon 14:49
+ Created: 2023-02-28 Tue 08:45
Validate
diff --git a/templator_front.html b/templator_front.html
index 1f52df2..2209727 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
@@ -1244,8 +1244,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
- 2.2.3 Python
+
+ 2.2.3 Python
# define TREXIO back ends
@@ -1260,8 +1260,8 @@ 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
@@ -1290,8 +1290,8 @@ 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
@@ -1447,8 +1447,8 @@ 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.
@@ -1504,8 +1504,8 @@ renaming the .txt data files.
-
- 2.5.1 C
+
+ 2.5.1 C
trexio_t*
@@ -1822,8 +1822,8 @@ renaming the .txt data files.
-
- 2.5.2 Fortran
+
+ 2.5.2 Fortran
interface
@@ -1841,8 +1841,8 @@ renaming the .txt data files.
-
- 2.5.3 Python
+
+ 2.5.3 Python
def _open(file_name: str, mode: str, back_end: int):
@@ -1890,8 +1890,8 @@ 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
@@ -1924,8 +1924,8 @@ 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.
@@ -1942,8 +1942,8 @@ output:
-
- 2.6.1 C
+
+ 2.6.1 C
trexio_exit_code
@@ -2028,8 +2028,8 @@ output:
-
- 2.6.2 Fortran
+
+ 2.6.2 Fortran
interface
@@ -2044,8 +2044,8 @@ output:
-
- 2.6.3 Python
+
+ 2.6.3 Python
def _close(trexio_file):
@@ -2063,8 +2063,8 @@ output:
-
- 2.7 File flushing
+
+ 2.7 File flushing
trexio_flush flushes all buffers into the trexio_t file.
@@ -2081,8 +2081,8 @@ output:
-
- 2.7.1 C
+
+ 2.7.1 C
trexio_exit_code
@@ -2123,8 +2123,8 @@ output:
-
- 2.7.2 Fortran
+
+ 2.7.2 Fortran
interface
@@ -2139,8 +2139,8 @@ output:
-
- 2.7.3 Python
+
+ 2.7.3 Python
def flush(trexio_file):
@@ -2158,8 +2158,8 @@ output:
-
- 2.8 File existence
+
+ 2.8 File existence
trexio_inquire check whether TREXIO file exists.
@@ -2196,8 +2196,8 @@ You can see examples of both functionalities in test_f.f90 (search
-
- 2.8.1 C
+
+ 2.8.1 C
trexio_exit_code
@@ -2227,8 +2227,8 @@ 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.
@@ -2248,8 +2248,8 @@ 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:
@@ -2268,8 +2268,8 @@ 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.
@@ -2291,8 +2291,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9.1 C
+
+ 2.9.1 C
@@ -2365,8 +2365,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9.2 Fortran
+
+ 2.9.2 Fortran
interface
@@ -2381,8 +2381,8 @@ 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):
@@ -2414,8 +2414,8 @@ 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.
@@ -2444,8 +2444,8 @@ output:
-
- 2.10.1 C
+
+ 2.10.1 C
trexio_exit_code
@@ -2489,8 +2489,8 @@ output:
-
- 2.10.2 Fortran
+
+ 2.10.2 Fortran
interface
@@ -2515,8 +2515,8 @@ output:
-
- 2.10.3 Python
+
+ 2.10.3 Python
See TREXIO File Python class.
@@ -2525,8 +2525,8 @@ See TREXIO File Python class.
-
- 2.11 Tasks to be done before closing
+
+ 2.11 Tasks to be done before closing
trexio_exit_code
@@ -2627,12 +2627,12 @@ 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:
@@ -2853,12 +2853,12 @@ 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
@@ -2888,8 +2888,8 @@ 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
@@ -2898,12 +2898,12 @@ 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
@@ -2940,8 +2940,8 @@ 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.
@@ -2961,8 +2961,8 @@ 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:
@@ -2989,12 +2989,12 @@ 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,
@@ -3065,8 +3065,8 @@ 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
@@ -3080,12 +3080,12 @@ 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
@@ -3149,8 +3149,8 @@ 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
@@ -3226,8 +3226,8 @@ 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
@@ -3282,8 +3282,8 @@ 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.
@@ -3375,8 +3375,8 @@ 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:
@@ -3449,12 +3449,12 @@ 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.
@@ -3536,8 +3536,8 @@ 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.
@@ -3548,12 +3548,12 @@ 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
@@ -3716,8 +3716,8 @@ 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
@@ -3868,11 +3868,11 @@ 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 */
@@ -4028,8 +4028,8 @@ 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
@@ -4104,8 +4104,8 @@ 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.
@@ -4197,8 +4197,8 @@ 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:
@@ -4370,12 +4370,12 @@ 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
@@ -4536,16 +4536,16 @@ 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);
@@ -7395,8 +7395,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.2 Fortran
+
+ 5.2 Fortran
interface
@@ -7456,8 +7456,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.3 Python
+
+ 5.3 Python
def info():
@@ -7564,8 +7564,8 @@ 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.
@@ -7814,7 +7814,7 @@ two code are identical, i.e. if the assert statement pass.
Author: TREX-CoE
- Created: 2023-02-27 Mon 14:48
+ Created: 2023-02-28 Tue 08:45
Validate
diff --git a/templator_hdf5.html b/templator_hdf5.html
index f4da194..8c3831b 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: 2023-02-27 Mon 14:48
+ Created: 2023-02-28 Tue 08:45
Validate
diff --git a/templator_text.html b/templator_text.html
index 36e73c9..8cf1916 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
@@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
-
- 4 Deinitialize function (templated part)
+
+ 4 Deinitialize function (templated part)
trexio_exit_code
@@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
-
- 5 Flush function (templated part)
+
+ 5 Flush function (templated part)
trexio_exit_code
@@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
-
- 6 Template for text read a group
+
+ 6 Template for text read a group
$group$_t*
@@ -845,8 +845,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
- 7 Template for text has a group
+
+ 7 Template for text has a group
trexio_exit_code
@@ -886,8 +886,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
- 8 Template for text flush a group
+
+ 8 Template for text flush a group
trexio_exit_code
@@ -951,8 +951,8 @@ 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.
@@ -1021,8 +1021,8 @@ 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
@@ -1085,8 +1085,8 @@ 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.
@@ -1182,8 +1182,8 @@ 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.
@@ -1284,8 +1284,8 @@ 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
@@ -1359,8 +1359,8 @@ 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
@@ -1650,8 +1650,8 @@ 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
@@ -1881,8 +1881,8 @@ 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
@@ -1910,8 +1910,8 @@ 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
@@ -2103,7 +2103,7 @@ Size specifies the number of data items, e.g. determinants.
Author: TREX-CoE
- Created: 2023-02-27 Mon 14:48
+ Created: 2023-02-28 Tue 08:45
Validate
diff --git a/trex.html b/trex.html
index 19d4b87..c05b59d 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.
-
+
@@ -724,15 +724,27 @@ defined in this group.
-
- 2.4 Electron (electron group)
+
+ 2.4 Electron (electron group)
+
+The chemical system consists of nuclei and electrons, where the
+nuclei are considered as fixed point charges with Cartesian
+coordinates. The wave function is stored in the spin-free
+formalism, and therefore, it is necessary for the user to
+explicitly store the number of electrons with spin up
+(\(N_\uparrow\)) and spin down (\(N_\downarrow\)). These numbers
+correspond to the normalization of the spin-up and spin-down
+single-particle reduced density matrices.
+
+
We consider wave functions expressed in the spin-free formalism, where
the number of ↑ and ↓ electrons is fixed.
-
+
+
@@ -778,8 +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
@@ -796,7 +808,7 @@ integrals, etc.
The id and current_label attributes need to be specified for each file.
-
+
@@ -857,21 +869,21 @@ 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, we enable
-the possibility to define dummy atoms to place basis functions in
-random positions.
+We consider here basis functions centered on nuclei. Hence, it is
+possibile to define dummy atoms to place basis functions in
+arbitrary positions.
@@ -920,8 +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
@@ -942,10 +954,10 @@ plane waves.
-
- 3.1.3 Data definitions
+
+ 3.1.3 Data definitions
-
+
@@ -1054,8 +1066,8 @@ plane waves.
-
- 3.1.4 Example
+
+ 3.1.4 Example
For example, consider H2 with the following basis set (in GAMESS
@@ -1133,8 +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
@@ -1166,7 +1178,7 @@ All the functions \(V_{A\ell}\) are parameterized as:
See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info.
-
+
@@ -1270,8 +1282,8 @@ 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
@@ -1334,8 +1346,8 @@ 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
@@ -1350,7 +1362,7 @@ The structure of this group is adapted for the
+
@@ -1467,71 +1479,93 @@ 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)
-
-Going from the atomic basis set to AOs implies a systematic
-construction of all the angular functions of each shell. We
-consider two cases for the angular functions: the real-valued
-spherical harmonics, and the polynomials in Cartesian coordinates.
-In the case of real spherical harmonics, the AOs are ordered as
-\(0, +1, -1, +2, -2, \dots, +m, -m\) (see Wikipedia).
-In the case of polynomials we
-impose the canonical (or alphabetical) ordering), i.e
-
-
-\begin{eqnarray}
-p & : & p_x, p_y, p_z \nonumber \\
-d & : & d_{xx}, d_{xy}, d_{xz}, d_{yy}, d_{yz}, d_{zz} \nonumber \\
-f & : & f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}, f_{xzz}, f_{yyy}, f_{yyz}, f_{yzz}, …f_{zzz} \nonumber \\
-{\rm etc.} \nonumber
-\end{eqnarray}
-
-
-Note that there is no exception for \(p\) orbitals in spherical
-coordinates: the ordering is \(0,+1,-1\) which corresponds \(p_z, p_x, p_y\).
-
-
AOs are defined as
\[
- \chi_i (\mathbf{r}) = \mathcal{N}_i\, P_{\eta(i)}(\mathbf{r})\, R_{s(i)} (\mathbf{r})
+ \chi_i (\mathbf{r}) = \mathcal{N}_i'\, P_{\eta(i)}(\mathbf{r})\, R_{s(i)} (\mathbf{r})
\]
-where \(i\) is the atomic orbital index,
-\(P\) encodes for either the
-polynomials or the spherical harmonics, \(s(i)\) returns the
-shell on which the AO is expanded, and \(\eta(i)\) denotes which
-angular function is chosen.
-\(\mathcal{N}_i\) is a normalization factor that enables the
-possibility to have different normalization coefficients within a
-shell, as in the GAMESS convention where
-\(\mathcal{N}_{x^2} \ne \mathcal{N}_{xy}\) because
-\[ \left[ \iiint \left(x-X_A \right)^2 R_{s(i)}
- (\mathbf{r}) dx\, dy\, dz \right]^{-1/2} \ne
- \left[ \iiint \left( x-X_A \right) \left( y-Y_A \right) R_{s(i)}
- (\mathbf{r}) dx\, dy\, dz \right]^{-1/2}. \]
+where \(i\) is the atomic orbital index, \(P\) refers to either
+polynomials or spherical harmonics, and \(s(i)\) specifies the shell
+on which the AO is expanded.
-In such a case, one should set the normalization of the shell (in
-the Basis set section) to \(\mathcal{N}_{z^2}\), which is the
-normalization factor of the atomic orbitals in spherical coordinates.
-The normalization factor of the \(xy\) function which should be
-introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
+\(\eta(i)\) denotes the chosen angular function. The AOs can be
+expressed using real spherical harmonics or polynomials in Cartesian
+coordinates. In the case of real spherical harmonics, the AOs are
+ordered as \(0, +1, -1, +2, -2, \dots, + m, -m\) (see Wikipedia). In
+the case of polynomials, the canonical (or alphabetical) ordering is
+used,
-
+
+
+
+
+
+
+
+
+
+
+| \(p\) |
+\(p_x, p_y, p_z\) |
+
+
+
+| \(d\) |
+\(d_{xx}, d_{xy}, d_{xz}, d_{yy}, d_{yz}, d_{zz}\) |
+
+
+
+| \(f\) |
+\(f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}\), |
+
+
+
+| |
+\(f_{xzz}, f_{yyy}, f_{yyz}, f_{yzz}, f_{zzz}\) |
+
+
+
+| \(\vdots\) |
+ |
+
+
+
+
+
+Note that for \(p\) orbitals in spherical coordinates, the ordering
+is \(0,+1,-1\) which corresponds to \(p_z, p_x, p_y\).
+
+
+
+\(\mathcal{N}_i'\) is a normalization factor that allows for different
+normalization coefficients within a single shell, as in the GAMESS
+convention where each individual function is unit-normalized.
+Using GAMESS convention, the normalization factor of the shell
+\(\mathcal{N}_d\) in the basis group is appropriate for instance
+for the \(d_z^2\) function (i.e.
+\(\mathcal{N}_{d}\equiv\mathcal{N}_{z^2}\)) but not for the \(d_{xy}\)
+AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
+ao groups is the ratio \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
+
+
+
+
@@ -1583,7 +1617,7 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
-
+
4.1.1 One-electron integrals (ao_1e_int group)
@@ -1601,7 +1635,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
-
+
@@ -1696,7 +1730,7 @@ over atomic orbitals.
-
+
4.1.2 Two-electron integrals (ao_2e_int group)
@@ -1722,7 +1756,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
-
+
@@ -1790,10 +1824,10 @@ The Cholesky decomposition of the integrals can also be stored:
-
- 4.2 Molecular orbitals (mo group)
+
+ 4.2 Molecular orbitals (mo group)
-
+
@@ -1880,8 +1914,8 @@ 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
@@ -1889,7 +1923,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -1984,8 +2018,8 @@ 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
@@ -1993,7 +2027,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -2062,12 +2096,12 @@ 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 \(\Psi\)
@@ -2109,7 +2143,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the examples.
-
+
@@ -2155,8 +2189,8 @@ 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
@@ -2178,7 +2212,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
-
+
@@ -2224,8 +2258,8 @@ 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
@@ -2296,7 +2330,7 @@ The order of the indices is chosen such that
- \(\dots\)
-
+
@@ -2377,8 +2411,8 @@ 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
@@ -2450,7 +2484,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
-
+
@@ -2581,22 +2615,22 @@ expressed in a basis of a one-electron function
-
- 6 Correlation factors
+
+ 6 Correlation factors
-
- 6.1 Jastrow factor (jastrow group)
+
+ 6.1 Jastrow factor (jastrow group)
-The Jastrow factor is an $N$-electron function to which the CI
-expansion is multiplied: \(\Psi = \Phi \times \exp(J)\),
+The Jastrow factor is an $N$-electron function which multiplies the CI
+expansion: \(\Psi = \Phi \times \exp(J)\),
In the following, we use the notations \(r_{ij} = |\mathbf{r}_i - \mathbf{r}_j|\) and
\(R_{i\alpha} = |\mathbf{r}_i - \mathbf{R}_\alpha|\), where indices
-\(i\) and \(j\) correspond to electrons and \(\alpha\) to nuclei.
+\(i\) and \(j\) refer to electrons and \(\alpha\) to nuclei.
@@ -2611,8 +2645,8 @@ following:
-
- 6.1.1 CHAMP
+
+ 6.1.1 CHAMP
The first form of Jastrow factor is the one used in
@@ -2627,53 +2661,76 @@ the CHAMP p
-\(J_{\text{eN}}\) contains electron-nucleus terms:
+\(J_{\text{eN}}\) contains electron-nucleus terms:
\[
- J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}}
- \frac{a_{1,\alpha}\, g_\alpha(R_{i\alpha})}{1+a_{2,\alpha}\, g_\alpha(R_{i\alpha})} +
- \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, [g_\alpha(R_{i\alpha})]^p - J_{eN}^\infty
+ J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}}\left[
+ \frac{a_{1,\alpha}\, f_\alpha(R_{i\alpha})}{1+a_{2,\alpha}\,
+ f_\alpha(R_{i\alpha})} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, [f_\alpha(R_{i\alpha})]^p - J_{\text{eN}}^\infty
+ \right]
\]
\(J_{\text{ee}}\) contains electron-electron terms:
+
+
+
\[
J_{\text{ee}}(\mathbf{r}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1}
- \frac{b_1\, f(r_{ij})}{1+b_2\, f(r_{ij})} +
- \sum_{p=2}^{N_\text{ord}^b} a_{p+1}\, [f(r_{ij})]^p - J_{ee}^\infty
+ \left[
+ \frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\, f_{\text{ee}}(r_{ij})}{1+b_2\, f_{\text{ee}}(r_{ij})} +
+ \sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, [f_{\text{ee}}(r_{ij})]^p - J_{\text{ee},ij}^\infty
+ \right]
\]
-and \(J_{\text{eeN}}\) contains electron-electron-Nucleus terms:
+\(\delta^{\uparrow\downarrow}_{ij}\) is zero when the electrons \(i\) and
+\(j\) have the same spin, and one otherwise.
+
+
+
+\(J_{\text{eeN}}\) contains electron-electron-Nucleus terms:
\[
- J_{\text{eeN}}(\mathbf{r},\mathbf{R}) =
+ J_{\text{eeN}}(\mathbf{r},\mathbf{R}) =
\sum_{\alpha=1}^{N_{\text{nucl}}}
\sum_{i=1}^{N_{\text{elec}}}
\sum_{j=1}^{i-1}
\sum_{p=2}^{N_{\text{ord}}}
\sum_{k=0}^{p-1}
\sum_{l=0}^{p-k-2\delta_{k,0}}
- c_{lkp\alpha} \left[ f({r}_{ij}) \right]^k
- \left[ \left[ g_\alpha({R}_{i\alpha}) \right]^l + \left[ g_\alpha({R}_{j\alpha}) \right]^l \right]
- \left[ g_\alpha({R}_{i\,\alpha}) \, g_\alpha({R}_{j\alpha}) \right]^{(p-k-l)/2}
+ c_{lkp\alpha} \left[ g_{\text{ee}}({r}_{ij}) \right]^k \nonumber \\
+ \left[ \left[ g_\alpha({R}_{i\alpha}) \right]^l + \left[ g_\alpha({R}_{j\alpha}) \right]^l \right]
+ \left[ g_\alpha({R}_{i\,\alpha}) \,
+ g_\alpha({R}_{j\alpha}) \right]^{(p-k-l)/2}
\]
-
-
-
\(c_{lkp\alpha}\) are non-zero only when \(p-k-l\) is even.
-The terms \(J_{\text{ee}}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to ensure that
-\(J_{\text{ee}}\) and \(J_{\text{eN}}\) have an asymptotic value of zero.
+The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to ensure that
+\(J_{\text{eN}}\) and \(J_{\text{ee}}\) have an asymptotic value of zero:
+
+
+
+\[
+ J_{\text{eN}}^{\infty} =
+ \frac{a_{1,\alpha}\, \kappa_\alpha^{-1}}{1+a_{2,\alpha}\,
+ \kappa_\alpha^{-1}} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, \kappa_\alpha^{-p}
+ \]
+\[
+ J_{\text{ee},ij}^{\infty} =
+ \frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\,
+ \kappa_{\text{ee}}^{-1}}{1+b_2\, \kappa_{\text{ee}}^{-1}} +
+ \sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, \kappa_{\text{ee}}^{-p}
+ \]
@@ -2682,20 +2739,21 @@ The terms \(J_{\text{ee}}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to en
\[
- f(r) = \frac{1-e^{-\kappa\, r}}{\kappa} \text{ and }
- g_\alpha(r) = e^{-\kappa_\alpha\, r}.
+ f_\alpha(r) = \frac{1-e^{-\kappa_\alpha\, r}}{\kappa_\alpha} \text{ and }
+ g_\alpha(r) = e^{-\kappa_\alpha\, r},
\]
-
- 6.1.2 Mu
+
+
+ 6.1.2 Mu
Mu-Jastrow is based on a one-parameter correlation factor that has
been introduced in the context of transcorrelated methods. This
-correlation factor imposes the electron-electron cusp and it is
+correlation factor imposes the electron-electron cusp, and it is
built such that the leading order in \(1/r_{12}\) of the effective
two-electron potential reproduces the long-range interaction of the
range-separated density functional theory. Its analytical
@@ -2710,19 +2768,19 @@ expression reads
-The electron-electron cusp is incorporated in the three-body term.
+The electron-electron cusp is incorporated in the three-body term
\[
J_\text{eeN} (\mathbf{r}, \mathbf{R}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) \,
- \Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha})
+ \Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha}),
\]
-\(u\) is an electron-electron function given by the symmetric function
+where ww\(u\) is an electron-electron function
@@ -2739,7 +2797,7 @@ electrons.
An envelope function has been introduced to cancel out the Jastrow
-effects between two-electrons when they are both close to a nucleus
+effects between two-electrons when at least one is close to a nucleus
(to perform a frozen-core calculation). The envelope function is
given by
@@ -2787,10 +2845,10 @@ The parameter \(\mu\) is stored in the ee array, the parameters
-
- 6.1.3 Table of values
+
+ 6.1.3 Table of values
-
+
@@ -2818,13 +2876,6 @@ The parameter \(\mu\) is stored in the ee array, the parameters
Type of Jastrow factor: CHAMP or Mu |
-
-ee_num |
-dim |
- |
-Number of Electron-electron parameters |
-
-
en_num |
dim |
@@ -2832,6 +2883,13 @@ The parameter \(\mu\) is stored in the ee array, the parameters
Number of Electron-nucleus parameters |
+
+ee_num |
+dim |
+ |
+Number of Electron-electron parameters |
+
+
een_num |
dim |
@@ -2839,13 +2897,6 @@ The parameter \(\mu\) is stored in the ee array, the parameters
Number of Electron-electron-nucleus parameters |
-
-ee |
-float |
-(jastrow.ee_num) |
-Electron-electron parameters |
-
-
en |
float |
@@ -2853,6 +2904,13 @@ The parameter \(\mu\) is stored in the ee array, the parameters
Electron-nucleus parameters |
+
+ee |
+float |
+(jastrow.ee_num) |
+Electron-electron parameters |
+
+
een |
float |
@@ -2894,8 +2952,8 @@ The parameter \(\mu\) is stored in the ee array, the parameters
-
- 7 Quantum Monte Carlo data (qmc group)
+
+ 7 Quantum Monte Carlo data (qmc group)
In quantum Monte Carlo calculations, the wave function is evaluated
@@ -2909,7 +2967,7 @@ By convention, the electron coordinates contain first all the electrons
of $↑$-spin and then all the $↓$-spin.
- |