From 30ac23da29b2546ddaf32c22463c3ecbe2171b11 Mon Sep 17 00:00:00 2001 From: q-posev <45995097+q-posev@users.noreply.github.com> Date: Sat, 17 Aug 2024 22:14:45 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20TREX-CoE?= =?UTF-8?q?/trexio@1a167aee7a3a70b937d36874b198365f007f5232=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 | 172 ++++++------ index.html | 4 +- intro.html | 4 +- lib.html | 58 ++-- templator_front.html | 650 +++++++++++++++++++++---------------------- templator_hdf5.html | 82 +++--- templator_text.html | 106 +++---- trex.html | 254 ++++++++--------- 9 files changed, 667 insertions(+), 667 deletions(-) diff --git a/README.html b/README.html index 0c95626..d048258 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 @@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.

Author: TREX-CoE

-

Created: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/examples.html b/examples.html index 62591d1..1e2d2eb 100644 --- a/examples.html +++ b/examples.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Examples @@ -346,61 +346,61 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Writing nuclear coordinates

+
+

1 Writing nuclear coordinates

Here is a demonstration of how to use TREXIO to write the nuclear @@ -410,8 +410,8 @@ as well as the necessary TREXIO functions to perform these actions.

-
-

1.1 C

+
+

1.1 C

#include <stdio.h>
@@ -461,8 +461,8 @@ as well as the necessary TREXIO functions to perform these actions.
-
-

1.2 Python

+
+

1.2 Python

This code uses the TREXIO Python binding to create a new TREXIO file named @@ -509,8 +509,8 @@ coordinates of the system.

-
-

1.3 Fortran

+
+

1.3 Fortran

program trexio_water
@@ -567,12 +567,12 @@ coordinates of the system.
-
-

2 Accessing sparse quantities (integrals)

+
+

2 Accessing sparse quantities (integrals)

-
-

2.1 Fortran

+
+

2.1 Fortran

program print_energy
@@ -618,8 +618,8 @@ One needs to read from the TREXIO file:
-
-

2.1.1 Declare Temporary variables

+
+

2.1.1 Declare Temporary variables

integer                       :: i, j, k, l, m
@@ -634,8 +634,8 @@ One needs to read from the TREXIO file:
-
-

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

+
+

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

call getarg(1, filename)
@@ -651,8 +651,8 @@ f = trexio_open (filename, 'r', TREXIO_AUTO
-
-

2.1.3 Read the nuclear repulsion energy

+
+

2.1.3 Read the nuclear repulsion energy

rc = trexio_read_nucleus_repulsion(f, E_nn)
@@ -666,8 +666,8 @@ f = trexio_open (filename, 'r', TREXIO_AUTO
-
-

2.1.4 Read the number of molecular orbitals

+
+

2.1.4 Read the number of molecular orbitals

rc = trexio_read_mo_num(f, n)
@@ -681,8 +681,8 @@ f = trexio_open (filename, 'r', TREXIO_AUTO
-
-

2.1.5 Allocate memory

+
+

2.1.5 Allocate memory

allocate( D(n,n), h0(n,n) )
@@ -694,8 +694,8 @@ W(:,:,:,:) = 0.d0
-
-

2.1.6 Read one-electron quantities

+
+

2.1.6 Read one-electron quantities

rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@@ -727,8 +727,8 @@ rc = trexio_read_rdm_1e(f, D)
-
-

2.1.7 Read two-electron quantities

+
+

2.1.7 Read two-electron quantities

Reading is done with OpenMP. Each thread reads its own buffer, and @@ -744,8 +744,8 @@ to be protected in the critical section when modified.

-
-
2.1.7.1 Electron repulsion integrals
+
+
2.1.7.1 Electron repulsion integrals
rc = trexio_has_mo_2e_int_eri(f)
@@ -794,8 +794,8 @@ icount = BUFSIZE
-
-
2.1.7.2 Reduced density matrix
+
+
2.1.7.2 Reduced density matrix
rc = trexio_has_rdm_2e(f)
@@ -839,8 +839,8 @@ icount = bufsize
-
-

2.1.8 Compute the energy

+
+

2.1.8 Compute the energy

When the orbitals are real, we can use @@ -886,8 +886,8 @@ E = E + E_nn

-
-

2.1.9 Terminate

+
+

2.1.9 Terminate

  deallocate( D, h0, G, W )
@@ -899,8 +899,8 @@ E = E + E_nn
-
-

2.2 Python

+
+

2.2 Python

import sys
@@ -934,8 +934,8 @@ One needs to read from the TREXIO file:
-
-

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

+
+

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

filename = sys.argv[1]
@@ -945,8 +945,8 @@ One needs to read from the TREXIO file:
-
-

2.2.2 Read the nuclear repulsion energy

+
+

2.2.2 Read the nuclear repulsion energy

E_nn = trexio.read_nucleus_repulsion(f)
@@ -955,8 +955,8 @@ One needs to read from the TREXIO file:
-
-

2.2.3 Read the number of molecular orbitals

+
+

2.2.3 Read the number of molecular orbitals

n = trexio.read_mo_num(f)
@@ -965,8 +965,8 @@ One needs to read from the TREXIO file:
-
-

2.2.4 Read one-electron quantities

+
+

2.2.4 Read one-electron quantities

if not trexio.has_mo_1e_int_core_hamiltonian(f):
@@ -985,12 +985,12 @@ One needs to read from the TREXIO file:
-
-

2.2.5 Read two-electron quantities

+
+

2.2.5 Read two-electron quantities

-
-
2.2.5.1 Electron repulsion integrals
+
+
2.2.5.1 Electron repulsion integrals
if not trexio.has_mo_2e_int_eri(f):
@@ -1020,8 +1020,8 @@ One needs to read from the TREXIO file:
-
-
2.2.5.2 Reduced density matrix
+
+
2.2.5.2 Reduced density matrix
if not trexio.has_rdm_2e(f):
@@ -1043,8 +1043,8 @@ One needs to read from the TREXIO file:
-
-

2.2.6 Compute the energy

+
+

2.2.6 Compute the energy

When the orbitals are real, we can use @@ -1073,12 +1073,12 @@ E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,

-
-

3 Reading determinants

+
+

3 Reading determinants

-
-

3.1 Fortran

+
+

3.1 Fortran

program test
@@ -1157,7 +1157,7 @@ end

Author: TREX-CoE

-

Created: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/index.html b/index.html index 0c95626..d048258 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 @@ -406,7 +406,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.

Author: TREX-CoE

-

Created: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/intro.html b/intro.html index cc7d03b..2aefc89 100644 --- a/intro.html +++ b/intro.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Motivation @@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.

Author: TREX-CoE

-

Created: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/lib.html b/lib.html index a2df6bf..a9eed68 100644 --- a/lib.html +++ b/lib.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + The TREXIO library @@ -346,19 +346,19 @@ for the JavaScript code in this tag.

Table of Contents

@@ -366,8 +366,8 @@ for the JavaScript code in this tag.
-
-

1 Format specification

+
+

1 Format specification

@@ -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.

-
-

2 The TREXIO library

+
+

2 The TREXIO library

@@ -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: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/templator_front.html b/templator_front.html index 8e49c9e..fe73d92 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: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/templator_hdf5.html b/templator_hdf5.html index 6b6cfd1..d54525a 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: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/templator_text.html b/templator_text.html index 5ceff1b..be05074 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: 2024-08-17 Sat 21:46

+

Created: 2024-08-17 Sat 22:14

Validate

diff --git a/trex.html b/trex.html index 9d33397..56595e8 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 @@ -346,72 +346,72 @@ for the JavaScript code in this tag.

Table of Contents

@@ -433,8 +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, @@ -444,7 +444,7 @@ have participated to the creation of the file, a list of authors of the file, and a textual description.

- +
@@ -537,19 +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.

-
+
@@ -634,15 +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.

-
+
@@ -726,10 +726,10 @@ used in periodic calculations. -
-

2.3 Periodic boundary calculations (pbc group)

+
+

2.3 Periodic boundary calculations (pbc group)

-
+
@@ -789,8 +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 @@ -809,7 +809,7 @@ the number of ↑ and ↓ electrons is fixed.

-
+
@@ -861,8 +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 @@ -879,7 +879,7 @@ integrals, etc. The id and current_label attributes need to be specified for each file.

-
+
@@ -956,16 +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 @@ -1019,8 +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 @@ -1084,8 +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 @@ -1106,8 +1106,8 @@ plane waves.

-
-

3.1.4 Oscillating orbitals

+
+

3.1.4 Oscillating orbitals

Basis functions can be made oscillating as @@ -1129,10 +1129,10 @@ Oscillation kind can be:

-
-

3.1.5 Data definitions

+
+

3.1.5 Data definitions

-
+
@@ -1384,8 +1384,8 @@ Oscillation kind can be: -
-

3.1.6 Example

+
+

3.1.6 Example

For example, consider H2 with the following basis set (in GAMESS @@ -1463,8 +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 @@ -1498,7 +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.

-
+
@@ -1613,8 +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 @@ -1677,8 +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 @@ -1693,7 +1693,7 @@ The structure of this group is adapted for the +

@@ -1826,12 +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 @@ -1912,7 +1912,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the

-
+
@@ -1971,7 +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)