From 3f8c54b04b094eefeb7c05862a56f60cbeee05b6 Mon Sep 17 00:00:00 2001 From: q-posev <45995097+q-posev@users.noreply.github.com> Date: Wed, 18 May 2022 09:56:52 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20TREX-CoE?= =?UTF-8?q?/trexio@24b1ce6b352a55d83da854a7b316af40c9c0ffdd=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.html | 4 +- examples.html | 82 +++---- index.html | 4 +- templator_front.html | 542 +++++++++++++++++++++---------------------- templator_hdf5.html | 70 +++--- templator_text.html | 88 +++---- trex.html | 192 +++++++-------- 7 files changed, 477 insertions(+), 505 deletions(-) diff --git a/README.html b/README.html index cda8f0b..8e2bede 100644 --- a/README.html +++ b/README.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREXIO source code documentation @@ -347,7 +347,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2022-05-06 Fri 09:09

+

Created: 2022-05-18 Wed 09:56

Validate

diff --git a/examples.html b/examples.html index 0dd6cad..0b3ec5a 100644 --- a/examples.html +++ b/examples.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Examples @@ -333,24 +333,24 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Accessing sparse quantities

+
+

1 Accessing sparse quantities

-
-

1.1 Fortran

+
+

1.1 Fortran

program print_energy
@@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
-
-

1.1.1 Declare Temporary variables

+
+

1.1.1 Declare Temporary variables

integer                       :: i, j, k, l, m
@@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
-
-

1.1.2 Obtain the name of the TREXIO file from the command line, and open it for reading

+
+

1.1.2 Obtain the name of the TREXIO file from the command line, and open it for reading

call getarg(1, filename)
@@ -444,8 +444,8 @@ f = trexio_open (filename, 'r', TREXIO_HDF5
-
-

1.1.3 Read the nuclear repulsion energy

+
+

1.1.3 Read the nuclear repulsion energy

rc = trexio_read_nucleus_repulsion(f, E_nn)
@@ -459,8 +459,8 @@ f = trexio_open (filename, 'r', TREXIO_HDF5
-
-

1.1.4 Read the number of molecular orbitals

+
+

1.1.4 Read the number of molecular orbitals

rc = trexio_read_mo_num(f, n)
@@ -474,8 +474,8 @@ f = trexio_open (filename, 'r', TREXIO_HDF5
-
-

1.1.5 Allocate memory

+
+

1.1.5 Allocate memory

allocate( D(n,n), h0(n,n) )
@@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
-
-

1.1.6 Read one-electron quantities

+
+

1.1.6 Read one-electron quantities

rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
-
-

1.1.7 Read two-electron quantities

+
+

1.1.7 Read two-electron quantities

Reading is done with OpenMP. Each thread reads its own buffer, and @@ -537,8 +537,8 @@ to be protected in the critical section when modified.

-
-
1.1.7.1 Electron repulsion integrals
+
+
1.1.7.1 Electron repulsion integrals
rc = trexio_has_mo_2e_int_eri(f)
@@ -587,8 +587,8 @@ icount = BUFSIZE
-
-
1.1.7.2 Reduced density matrix
+
+
1.1.7.2 Reduced density matrix
rc = trexio_has_rdm_2e(f)
@@ -632,8 +632,8 @@ icount = bufsize
-
-

1.1.8 Compute the energy

+
+

1.1.8 Compute the energy

When the orbitals are real, we can use @@ -679,8 +679,8 @@ E = E + E_nn

-
-

1.1.9 Terminate

+
+

1.1.9 Terminate

  deallocate( D, h0, G, W )
@@ -695,7 +695,7 @@ E = E + E_nn

Author: TREX-CoE

-

Created: 2022-05-06 Fri 09:09

+

Created: 2022-05-18 Wed 09:56

Validate

diff --git a/index.html b/index.html index cda8f0b..8e2bede 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREXIO source code documentation @@ -347,7 +347,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2022-05-06 Fri 09:09

+

Created: 2022-05-18 Wed 09:56

Validate

diff --git a/templator_front.html b/templator_front.html index f46e07b..f525e22 100644 --- a/templator_front.html +++ b/templator_front.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Front end API @@ -333,174 +333,174 @@ 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
    • @@ -515,8 +515,8 @@ 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 @@ -552,8 +552,8 @@ The maximum string size for the filenames is 4096 characters.

-
-

2 Front end

+
+

2 Front end

All calls to TREXIO are thread-safe. @@ -561,10 +561,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.

-
-

2.1 Error handling

+
+

2.1 Error handling

- +
@@ -853,8 +853,8 @@ 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 @@ -880,8 +880,8 @@ 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*
@@ -1016,8 +1016,8 @@ and the corresponding message are not propagated to the source code.
-
-
2.1.1.2 Fortran interface
+
+
2.1.1.2 Fortran interface
interface
@@ -1033,8 +1033,8 @@ 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):
@@ -1067,8 +1067,8 @@ and the corresponding message are not propagated to the source code.
-
-

2.2 Back ends

+
+

2.2 Back ends

TREXIO has several back ends: @@ -1097,8 +1097,8 @@ 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;
@@ -1147,8 +1147,8 @@ 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
@@ -1189,8 +1189,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
-

2.2.3 Python

+
+

2.2.3 Python

# define TREXIO back ends
@@ -1205,8 +1205,8 @@ 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 @@ -1235,8 +1235,8 @@ 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 @@ -1392,8 +1392,8 @@ to work with TREXIO files.

-
-

2.5 TODO (Remove) : Polymorphism of the file handle

+
+

2.5 TODO (Remove) : Polymorphism of the file handle

Polymorphism of the trexio_t type is handled by ensuring that the @@ -1412,8 +1412,8 @@ corresponding types for all back ends can be safely casted to

-
-

2.6 File opening

+
+

2.6 File opening

trexio_open creates a new TREXIO file or opens the existing one. @@ -1469,8 +1469,8 @@ renaming the .txt data files.

-
-

2.6.1 C

+
+

2.6.1 C

trexio_t*
@@ -1787,8 +1787,8 @@ renaming the .txt data files.
-
-

2.6.2 Fortran

+
+

2.6.2 Fortran

interface
@@ -1806,8 +1806,8 @@ renaming the .txt data files.
-
-

2.6.3 Python

+
+

2.6.3 Python

def _open(file_name: str, mode: str, back_end: int):
@@ -1855,8 +1855,8 @@ renaming the .txt data files.
-
-

2.6.4 Zero-based versus one-based arrays of indices

+
+

2.6.4 Zero-based versus one-based arrays of indices

Because arrays are zero-based in Fortran, we need to set a flag to @@ -1889,8 +1889,8 @@ know if we need to shift by 1 arrays of indices.

-
-

2.7 File closing

+
+

2.7 File closing

trexio_close closes an existing trexio_t file. @@ -1907,8 +1907,8 @@ output:

-
-

2.7.1 C

+
+

2.7.1 C

trexio_exit_code
@@ -1993,8 +1993,8 @@ output:
-
-

2.7.2 Fortran

+
+

2.7.2 Fortran

interface
@@ -2009,8 +2009,8 @@ output:
-
-

2.7.3 Python

+
+

2.7.3 Python

def _close(trexio_file):
@@ -2028,8 +2028,8 @@ output:
-
-

2.8 File existence

+
+

2.8 File existence

trexio_inquire check whether TREXIO file exists. @@ -2066,8 +2066,8 @@ You can see examples of both functionalities in test_f.f90 (search

-
-

2.8.1 C

+
+

2.8.1 C

trexio_exit_code
@@ -2097,8 +2097,8 @@ 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. @@ -2118,8 +2118,8 @@ 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:
@@ -2138,8 +2138,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
-

2.9 File state

+
+

2.9 File state

trexio_set_state set an existing trexio_t file handle to a given state. @@ -2158,8 +2158,8 @@ output:

-
-

2.9.1 C

+
+

2.9.1 C

trexio_exit_code
@@ -2187,8 +2187,8 @@ output:
-
-

2.9.2 Fortran

+
+

2.9.2 Fortran

interface
@@ -2213,8 +2213,8 @@ output:
-
-

2.9.3 Python

+
+

2.9.3 Python

See TREXIO File Python class. @@ -2223,8 +2223,8 @@ See TREXIO File Python class.

-
-

2.10 Tasks to be done before closing

+
+

2.10 Tasks to be done before closing

trexio_exit_code
@@ -2325,12 +2325,12 @@ 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: @@ -2551,12 +2551,12 @@ value will result in TREXIO_INVALID_ARG_2 exit code.

-
-

3.2 Templates for front end has/read/write a single numerical attribute

+
+

3.2 Templates for front end has/read/write a single numerical attribute

-
-

3.2.1 Introduction

+
+

3.2.1 Introduction

This section concerns API calls related to numerical attributes, @@ -2627,8 +2627,8 @@ namely single value of int/float types.

-
-

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 @@ -2642,12 +2642,12 @@ precision (see Table above).

-
-
3.2.2.1 Function declarations
+
+
3.2.2.1 Function declarations
-
-
3.2.2.2 Source code for double precision functions
+
+
3.2.2.2 Source code for double precision functions
trexio_exit_code
@@ -2711,8 +2711,8 @@ precision (see Table above).
-
-
3.2.2.3 Source code for single precision functions
+
+
3.2.2.3 Source code for single precision functions
trexio_exit_code
@@ -2788,8 +2788,8 @@ precision (see Table above).
-
-
3.2.2.4 Source code for default functions
+
+
3.2.2.4 Source code for default functions
trexio_exit_code
@@ -2844,8 +2844,8 @@ precision (see Table above).
-
-

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. @@ -2937,8 +2937,8 @@ 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 write_$group_num$(trexio_file, num_w: $group_num_py_dtype$) -> None:
@@ -3011,12 +3011,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

3.3 Templates for front end has/read/write a dataset of numerical data

+
+

3.3 Templates for front end has/read/write a dataset of numerical data

-
-

3.3.1 Introduction

+
+

3.3.1 Introduction

This section concerns API calls related to datasets. @@ -3098,8 +3098,8 @@ This section concerns API calls related to datasets.

-
-

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 functions can be found below. @@ -3110,12 +3110,12 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble

-
-
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
@@ -3278,8 +3278,8 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
-
3.3.2.3 Source code for single precision functions
+
+
3.3.2.3 Source code for single precision functions
trexio_exit_code
@@ -3430,11 +3430,11 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
-
3.3.2.4 Source code for memory-safe functions
+
+
3.3.2.4 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 */
@@ -3590,8 +3590,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
-
-
3.3.2.5 Source code for default functions
+
+
3.3.2.5 Source code for default functions
trexio_exit_code
@@ -3666,8 +3666,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
-
-

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. @@ -3759,8 +3759,8 @@ 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_$group_dset$(trexio_file, dset_w) -> None:
@@ -3937,12 +3937,12 @@ 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 sparse data

+
+

3.4 Templates for front end has/read/write a dataset of sparse data

-
-

3.4.1 Introduction

+
+

3.4.1 Introduction

Sparse data structures are used typically for large tensors such as @@ -4103,16 +4103,16 @@ This section concerns API calls related to sparse data structures.

-
-

3.4.2 C templates for front end

+
+

3.4.2 C templates for front end

-
-
3.4.2.1 Function declarations
+
+
3.4.2.1 Function declarations
-
-
3.4.2.2 Source code for default functions
+
+
3.4.2.2 Source code for default functions
trexio_exit_code trexio_read_safe_$group_dset$(trexio_t* const file,
@@ -4388,8 +4388,8 @@ This section concerns API calls related to sparse data structures.
-
-

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. @@ -4490,8 +4490,8 @@ 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: File, offset_file: int, buffer_size: int, indices: list, values: list) -> None:
@@ -4703,12 +4703,12 @@ 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 strings

+
+

3.5 Templates for front end has/read/write a dataset of strings

-
-

3.5.1 Introduction

+
+

3.5.1 Introduction

This section concerns API calls related to datasets of strings. @@ -4748,8 +4748,8 @@ This section concerns API calls related to datasets of strings.

-
-

3.5.2 C templates for front end

+
+

3.5.2 C templates for front end

First parameter is the TREXIO file handle. Second parameter is the variable to be written/read @@ -4757,12 +4757,12 @@ to/from the TREXIO file (except for trexio_has_ functi

-
-
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
@@ -5012,8 +5012,8 @@ to/from the TREXIO file (except for trexio_has_ functi
-
-

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. @@ -5112,8 +5112,8 @@ 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, dset_w: list) -> None:
@@ -5211,12 +5211,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

3.6 Templates for front end has/read/write a single string attribute

+
+

3.6 Templates for front end has/read/write a single string attribute

-
-

3.6.1 Introduction

+
+

3.6.1 Introduction

This section concerns API calls related to string attributes. @@ -5256,16 +5256,16 @@ This section concerns API calls related to string attributes.

-
-

3.6.2 C templates for front end

+
+

3.6.2 C templates for front end

-
-
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
@@ -5369,8 +5369,8 @@ This section concerns API calls related to string attributes.
-
-

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. @@ -5450,8 +5450,8 @@ 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_$group_str$(trexio_file, str_w: str) -> None:
@@ -5526,12 +5526,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

3.7 Templates for front end delete an entire group (UNSAFE MODE)

+
+

3.7 Templates for front end delete an entire group (UNSAFE MODE)

-
-

3.7.1 Introduction

+
+

3.7.1 Introduction

This section concerns API calls related to string attributes. @@ -5561,8 +5561,8 @@ This section concerns API calls related to string attributes.

-
-

3.7.2 C templates for front end

+
+

3.7.2 C templates for front end

trexio_exit_code
@@ -5597,8 +5597,8 @@ This section concerns API calls related to string attributes.
-
-

3.7.3 Fortran templates for front end

+
+

3.7.3 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -5618,8 +5618,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.7.4 Python templates for front end

+
+

3.7.4 Python templates for front end

def delete_$group$(trexio_file) -> None:
@@ -5644,8 +5644,8 @@ 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, @@ -5716,8 +5716,8 @@ This section concerns API calls related to Slater determinants.

-
-

4.0.1 C source code

+
+

4.0.1 C source code

trexio_exit_code
@@ -6082,8 +6082,8 @@ 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. @@ -6240,8 +6240,8 @@ 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:
@@ -6585,8 +6585,8 @@ 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. @@ -6620,8 +6620,8 @@ of the determinant and returns two list of orbitals each corresponding to a diff

-
-

5.1 C

+
+

5.1 C

trexio_exit_code trexio_info(void);
@@ -6816,8 +6816,8 @@ of the determinant and returns two list of orbitals each corresponding to a diff
-
-

5.2 Fortran

+
+

5.2 Fortran

interface
@@ -6858,8 +6858,8 @@ of the determinant and returns two list of orbitals each corresponding to a diff
-
-

5.3 Python

+
+

5.3 Python

def info():
@@ -6935,8 +6935,8 @@ of the determinant and returns two list of orbitals each corresponding to a diff
-
-

6 Fortran helper/wrapper functions

+
+

6 Fortran helper/wrapper functions

The function below adapts the original C-based trexio_open for Fortran. @@ -7088,7 +7088,7 @@ two code are identical, i.e. if the assert statement pass.

Author: TREX-CoE

-

Created: 2022-05-06 Fri 09:09

+

Created: 2022-05-18 Wed 09:56

Validate

diff --git a/templator_hdf5.html b/templator_hdf5.html index cc5a9b0..7a99f10 100644 --- a/templator_hdf5.html +++ b/templator_hdf5.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + HDF5 back end @@ -311,23 +311,23 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Template for HDF5 definitions

+
+

1 Template for HDF5 definitions

#define $GROUP$_GROUP_NAME          "$group$"
@@ -339,8 +339,8 @@ for the JavaScript code in this tag.
-
-

2 Template for HDF5 structures

+
+

2 Template for HDF5 structures

typedef struct trexio_hdf5_s {
@@ -353,8 +353,8 @@ for the JavaScript code in this tag.
-
-

3 Template for HDF5 init/deinit

+
+

3 Template for HDF5 init/deinit

trexio_exit_code
@@ -459,8 +459,8 @@ for the JavaScript code in this tag.
-
-

4 Template for HDF5 has/read/write a numerical attribute

+
+

4 Template for HDF5 has/read/write a numerical attribute

trexio_exit_code
@@ -564,8 +564,8 @@ for the JavaScript code in this tag.
-
-

5 Template for HDF5 has/read/write a dataset of numerical data

+
+

5 Template for HDF5 has/read/write a dataset of numerical data

trexio_exit_code
@@ -699,8 +699,8 @@ for the JavaScript code in this tag.
-
-

6 Template for HDF5 has/read/write a dataset of sparse data

+
+

6 Template for HDF5 has/read/write a dataset of sparse data

Sparse data is stored using extensible datasets of HDF5. Extensibility is required @@ -903,8 +903,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s

-
-

7 Template for HDF5 has/read/write a dataset of strings

+
+

7 Template for HDF5 has/read/write a dataset of strings

trexio_exit_code
@@ -1102,8 +1102,8 @@ 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 string attribute

+
+

8 Template for HDF5 has/read/write a string attribute

trexio_exit_code
@@ -1230,8 +1230,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
-

9 Template for HDF5 delete a group (UNSAFE mode)

+
+

9 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 @@ -1271,8 +1271,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of

-
-

10 Source code for the determinant part

+
+

10 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. @@ -1525,8 +1525,8 @@ Size specifies the number of data items (e.g. determinants) to process.

-
-

11 Helper functions

+
+

11 Helper functions

trexio_exit_code
@@ -1789,7 +1789,7 @@ Size specifies the number of data items (e.g. determinants) to process.

Author: TREX-CoE

-

Created: 2022-05-06 Fri 09:09

+

Created: 2022-05-18 Wed 09:56

Validate

diff --git a/templator_text.html b/templator_text.html index 935c3c2..acdf922 100644 --- a/templator_text.html +++ b/templator_text.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TEXT back end @@ -311,20 +311,20 @@ for the JavaScript code in this tag.

Table of Contents

@@ -346,8 +346,8 @@ 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 {
@@ -366,8 +366,8 @@ 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

typedef struct trexio_text_s {
@@ -380,8 +380,8 @@ The file is written when closed, or when the flush function is called.
-
-

3 Initialize function (constant part)

+
+

3 Initialize function (constant part)

trexio_exit_code
@@ -524,8 +524,8 @@ The file is written when closed, or when the flush function is called.
-
-

4 Deinitialize function (templated part)

+
+

4 Deinitialize function (templated part)

trexio_exit_code
@@ -547,8 +547,8 @@ The file is written when closed, or when the flush function is called.
-
-

5 Template for text read a group

+
+

5 Template for text read a group

$group$_t*
@@ -849,8 +849,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

6 Template for text flush a group

+
+

6 Template for text flush a group

trexio_exit_code
@@ -914,8 +914,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

7 Template for text free memory

+
+

7 Template for text free memory

Memory is allocated when reading. The following function frees memory. @@ -962,8 +962,8 @@ Memory is allocated when reading. The following function frees memory.

-
-

8 Template for has/read/write a numerical attribute

+
+

8 Template for has/read/write a numerical attribute

trexio_exit_code
@@ -1026,8 +1026,8 @@ Memory is allocated when reading. The following function frees memory.
-
-

9 Template for has/read/write a dataset of numerical data

+
+

9 Template for has/read/write a dataset of numerical data

The group_dset array is assumed allocated with the appropriate size. @@ -1123,8 +1123,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

10 Template for has/read/write a dataset of strings

+
+

10 Template for has/read/write a dataset of strings

The group_dset array is assumed allocated with the appropriate size. @@ -1225,8 +1225,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

11 Template for has/read/write a string attribute

+
+

11 Template for has/read/write a string attribute

trexio_exit_code
@@ -1300,8 +1300,8 @@ The group_dset array is assumed allocated with the appropriate size
-
-

12 Template for has/read/write the dataset of sparse data

+
+

12 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 @@ -1575,8 +1575,8 @@ User provides indices and values of the sparse array as two separate variables.

-
-

13 Template for text delete a group (UNSAFE mode)

+
+

13 Template for text delete a group (UNSAFE mode)

trexio_exit_code
@@ -1604,8 +1604,8 @@ User provides indices and values of the sparse array as two separate variables.
-
-

14 Source code for the determinant part

+
+

14 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 @@ -2009,7 +2009,7 @@ Size specifies the number of data items, e.g. determinants.

Author: TREX-CoE

-

Created: 2022-05-06 Fri 09:09

+

Created: 2022-05-18 Wed 09:56

Validate

diff --git a/trex.html b/trex.html index 68311cd..2270815 100644 --- a/trex.html +++ b/trex.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREX Configuration file @@ -333,35 +333,35 @@ for the JavaScript code in this tag.

Table of Contents

@@ -390,6 +390,10 @@ variables cannot be negative. This additional constraint is required because dim attributes are used internally to allocate memory and to check array boundaries in the memory-safe API. Most of the times, the dim variables contain the num suffix. +You may also encounter some dim readonly variables. +It means that the value is automatically computed and written by the +TREXIO library, thus it is read-only and cannot be (over)written by the +user.

@@ -407,8 +411,8 @@ the examples.

-
-

1 Metadata (metadata group)

+
+

1 Metadata (metadata group)

As we expect our files to be archived in open-data repositories, we @@ -418,7 +422,7 @@ which have participated to the creation of the file, a list of authors of the file, and a textual description.

- +
@@ -499,15 +503,15 @@ then the unsafe attribute value can be manually overwritten (in uns -
-

2 Electron (electron group)

+
+

2 Electron (electron group)

We consider wave functions expressed in the spin-free formalism, where the number of ↑ and ↓ electrons is fixed.

-
+
@@ -553,15 +557,15 @@ the number of ↑ and ↓ electrons is fixed. -
-

3 Nucleus (nucleus group)

+
+

3 Nucleus (nucleus group)

The nuclei are considered as fixed point charges. Coordinates are given in Cartesian \((x,y,z)\) format.

-
+
@@ -628,8 +632,8 @@ given in Cartesian \((x,y,z)\) format. -
-

4 Effective core potentials (ecp group)

+
+

4 Effective core potentials (ecp group)

An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the @@ -662,7 +666,7 @@ 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.

-
+
@@ -764,8 +768,8 @@ If you encounter the aforementioned issue, please report it to our -

4.1 Example

+
+

4.1 Example

For example, consider H2 molecule with the following @@ -828,8 +832,8 @@ power = [

-
-

5 Basis set (basis group)

+
+

5 Basis set (basis group)

We consider here basis functions centered on nuclei. Hence, we enable @@ -882,7 +886,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\). All the basis set parameters are stored in one-dimensional arrays:

-
+
@@ -976,8 +980,8 @@ All the basis set parameters are stored in one-dimensional arrays:
-
-

5.1 Example

+
+

5.1 Example

For example, consider H2 with the following basis set (in GAMESS @@ -1055,8 +1059,8 @@ prim_factor =

-
-

6 Atomic orbitals (ao group)

+
+

6 Atomic orbitals (ao group)

Going from the atomic basis set to AOs implies a systematic @@ -1109,13 +1113,13 @@ shell, as in the GAMESS convention where

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 +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 \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).

- +
@@ -1167,8 +1171,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
-
-

6.1 One-electron integrals (ao_1e_int group)

+
+

6.1 One-electron integrals (ao_1e_int group)

  • \[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}} @@ -1185,7 +1189,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are over atomic orbitals.

    - +
    @@ -1245,8 +1249,8 @@ over atomic orbitals. -
    -

    6.2 Two-electron integrals (ao_2e_int group)

    +
    +

    6.2 Two-electron integrals (ao_2e_int group)

    The two-electron integrals for a two-electron operator \(\hat{O}\) are @@ -1267,7 +1271,7 @@ notation. \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential -

    +
    @@ -1307,10 +1311,10 @@ notation. -
    -

    7 Molecular orbitals (mo group)

    +
    +

    7 Molecular orbitals (mo group)

    -
    +
    @@ -1376,8 +1380,8 @@ notation.
-
-

7.1 One-electron integrals (mo_1e_int group)

+
+

7.1 One-electron integrals (mo_1e_int group)

The operators as the same as those defined in the @@ -1385,7 +1389,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

- +
@@ -1445,8 +1449,8 @@ the basis of molecular orbitals. -
-

7.2 Two-electron integrals (mo_2e_int group)

+
+

7.2 Two-electron integrals (mo_2e_int group)

The operators as the same as those defined in the @@ -1454,7 +1458,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

-
+
@@ -1494,8 +1498,8 @@ the basis of molecular orbitals. -
-

8 Slater determinants (determinant group)

+
+

8 Slater determinants (determinant group)

The configuration interaction (CI) wave function \(\Psi\) @@ -1504,63 +1508,31 @@ can be expanded in the basis of Slater determinants \(D_I\) as follows

\[ -

-
- - --- -- - - - - - - -
Ψ> = ∑I CIDI>
-

-\] + \Psi = \sum_I C_I D_I + \]

-For relatively small expansions, a given determinant can be represented as a list of mo.num occupation numbers. -However, this requires a lot of extra memory and would be technically impossible for larger expansions -(millions of determinants). This is why the determinants are stored as bit fields in the TREXIO file - (see ~int bitfield type in the table below). By default, the chemist notation is used, namely +For relatively small expansions, a given determinant can be represented as a list of occupied orbitals. +However, this becomes unfeasible for larger expansions and requires more advanced data structures. +The bit field representation is used here, namely a given determinant is represented as \(N_{\text{int}}\) +64-bit integers where j-th bit is set to 1 if there is an electron in the j-th orbital and 0 otherwise. +This gives access to larger determinant expansions by optimising the storage of the determinant lists +in the memory.

\[ -

- - - --- -- - - - - - - -
DI > =α1 α2 \ldots αn↑ β1 β2 \ldots βn↓ >
-

-\] + D_I = \alpha_1 \alpha_2 \ldots \alpha_{n\uparrow} \beta_1 \beta_2 \ldots \beta_{n\downarrow} + \]

where \(\alpha\) and \(\beta\) denote $↑$-spin and $↓$-spin electrons, respectively, \(n\uparrow\) and \(n\downarrow\) correspond to electron.up_num and electron.dn_num, respectively. -Internally, bit fields for \(\alpha\) and \(\beta\) electrons are stored separately, -which is why the determinant.list attribute has a second dimension.

- +
@@ -1583,7 +1555,7 @@ which is why the determinant.list attribute has a second dimension. - + @@ -1606,8 +1578,8 @@ which is why the determinant.list attribute has a second dimension. -
-

9 Excited states (state group)

+
+

9 Excited states (state group)

By default, the determinant group corresponds to the ground state. @@ -1616,7 +1588,7 @@ correspond to excited state wave functions for the same set of determinants. This is the goal of the present group

-
numdimdim readonly   Number of determinants
+
@@ -1655,8 +1627,8 @@ determinants. This is the goal of the present group -
-

10 Reduced density matrices (rdm group)

+
+

10 Reduced density matrices (rdm group)

The reduced density matrices are defined in the basis of molecular @@ -1709,7 +1681,7 @@ The total energy can be computed as: \]

-
+
@@ -1790,8 +1762,8 @@ The total energy can be computed as: -
-

11 Quantum Monte Carlo data (qmc group)

+
+

11 Quantum Monte Carlo data (qmc group)

In quantum Monte Carlo calculations, the wave function is evaluated @@ -1805,7 +1777,7 @@ By convention, the electron coordinates contain first all the electrons of $↑$-spin and then all the $↓$-spin.

-
+
@@ -1860,7 +1832,7 @@ of $↑$-spin and then all the $↓$-spin.

Author: TREX-CoE

-

Created: 2022-05-06 Fri 09:09

+

Created: 2022-05-18 Wed 09:56

Validate