From e6d825e1fd0ba3031384f0fa047ee1df55a39409 Mon Sep 17 00:00:00 2001 From: scemama Date: Thu, 15 Jul 2021 12:45:22 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20TREX-CoE?= =?UTF-8?q?/trexio@90860ea1e01d9472fa24950270b1237ed308b4f8=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.html | 4 +- Sparse.html | 16 ++-- index.html | 4 +- templator_front.html | 174 +++++++++++++++++++++---------------------- templator_hdf5.html | 52 ++++++------- templator_text.html | 112 ++++++++++++++-------------- trex.html | 118 ++++++++++++++--------------- 7 files changed, 240 insertions(+), 240 deletions(-) diff --git a/README.html b/README.html index 61ae249..b41db28 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 @@ -342,7 +342,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2021-06-25 Fri 12:16

+

Created: 2021-07-15 Thu 12:45

Validate

diff --git a/Sparse.html b/Sparse.html index 68f3df3..548a3c7 100644 --- a/Sparse.html +++ b/Sparse.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + ‎ @@ -232,8 +232,8 @@ for the JavaScript code in this tag.

Table of Contents

@@ -241,8 +241,8 @@ for the JavaScript code in this tag. See templatorfront.org

-
-

1 Text back end

+
+

1 Text back end

As the size of the dataset should be extensible, the simplest @@ -256,8 +256,8 @@ The offset can be used with fseek(69L*offset, SEEK_SET)

-
-

2 HDF5 Back end

+
+

2 HDF5 Back end

We need to declare the number of rows of the dataset as @@ -278,7 +278,7 @@ If the offset+num > nmax, we need to extend the dataset.

-

Created: 2021-06-25 Fri 12:16

+

Created: 2021-07-15 Thu 12:45

Validate

diff --git a/index.html b/index.html index 61ae249..b41db28 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 @@ -342,7 +342,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2021-06-25 Fri 12:16

+

Created: 2021-07-15 Thu 12:45

Validate

diff --git a/templator_front.html b/templator_front.html index 77903e8..552c943 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 @@ -333,61 +333,61 @@ 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
    • @@ -402,8 +402,8 @@ 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 @@ -438,8 +438,8 @@ The maximum string size for the filenames is 4096 characters.

-
-

2 Front end

+
+

2 Front end

All calls to TREXIO are thread-safe. @@ -447,10 +447,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.

-
-

2.1 Error handling

+
+

2.1 Error handling

- +
@@ -750,8 +750,8 @@ The text strings are extracted from the previous table. -
-

2.2 Back ends

+
+

2.2 Back ends

TREXIO has several back ends: @@ -783,8 +783,8 @@ lines that correspond to the TREXIO_JSON back end (not implemented

-
-

2.3 Read/write behavior

+
+

2.3 Read/write behavior

Every time a reading function is called, the data is read from the @@ -812,8 +812,8 @@ 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 @@ -846,8 +846,8 @@ TREXIO files will have as a first argument the TREXIO file handle.

-
-

2.5 Polymorphism of the file handle

+
+

2.5 Polymorphism of the file handle

Polymorphism of the trexio_t type is handled by ensuring that the @@ -866,8 +866,8 @@ 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 existing one. @@ -1058,8 +1058,8 @@ 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. @@ -1155,12 +1155,12 @@ output:

-
-

3 Templates for front end

+
+

3 Templates for front end

-
-

3.1 Description

+
+

3.1 Description

Consider the following block of trex.json: @@ -1350,8 +1350,8 @@ or double precision for integer and floating point numbers.

-
-

3.2 Templates for front end has/read/write a single dimensioning variable

+
+

3.2 Templates for front end has/read/write a single dimensioning variable

This section concerns API calls related to dimensioning variables. @@ -1420,8 +1420,8 @@ This section concerns API calls related to dimensioning variables.

-
-

3.2.1 C templates for front end

+
+

3.2.1 C templates for front end

The C templates that correspond to each of the abovementioned @@ -1610,8 +1610,8 @@ precision (see Table above).

-
-

3.2.2 Fortran templates for front end

+
+

3.2.2 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -1697,8 +1697,8 @@ 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

This section concerns API calls related to datasets. @@ -1767,8 +1767,8 @@ This section concerns API calls related to datasets.

-
-

3.3.1 C templates for front end

+
+

3.3.1 C templates for front end

The C templates that correspond to each of the abovementioned functions can be found below. @@ -2087,8 +2087,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T

-
-

3.3.2 Fortran templates for front end

+
+

3.3.2 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -2174,8 +2174,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.4 Sparse data structures

+
+

3.4 Sparse data structures

Sparse data structures are used typically for large tensors such as @@ -2316,12 +2316,12 @@ For the values,

-
-

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. @@ -2361,8 +2361,8 @@ 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 @@ -2605,8 +2605,8 @@ 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. @@ -2703,12 +2703,12 @@ 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. @@ -2748,8 +2748,8 @@ 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

trexio_exit_code
@@ -2849,8 +2849,8 @@ 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. @@ -2929,8 +2929,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

4 Fortran helper/wrapper functions

+
+

4 Fortran helper/wrapper functions

The function below adapts the original C-based trexio_open for Fortran. @@ -3064,7 +3064,7 @@ two code are identical, i.e. if the assert statement pass.

Author: TREX-CoE

-

Created: 2021-06-25 Fri 12:16

+

Created: 2021-07-15 Thu 12:45

Validate

diff --git a/templator_hdf5.html b/templator_hdf5.html index 46e00c3..f8a9ef1 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 @@ -311,27 +311,27 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 HDF5 back end

+
+

1 HDF5 back end

-
-

1.1 Template for HDF5 definitions

+
+

1.1 Template for HDF5 definitions

#define $GROUP$_GROUP_NAME          "$group$"
@@ -343,8 +343,8 @@ for the JavaScript code in this tag.
-
-

1.2 Template for HDF5 structures

+
+

1.2 Template for HDF5 structures

typedef struct trexio_hdf5_s {
@@ -359,8 +359,8 @@ for the JavaScript code in this tag.
-
-

1.3 Template for HDF5 init/deinit

+
+

1.3 Template for HDF5 init/deinit

trexio_exit_code
@@ -440,8 +440,8 @@ for the JavaScript code in this tag.
-
-

1.4 Template for HDF5 has/read/write a single dimensioning variable

+
+

1.4 Template for HDF5 has/read/write a single dimensioning variable

trexio_exit_code
@@ -557,8 +557,8 @@ for the JavaScript code in this tag.
-
-

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

+
+

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

trexio_exit_code
@@ -687,8 +687,8 @@ for the JavaScript code in this tag.
-
-

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

+
+

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

trexio_exit_code
@@ -892,8 +892,8 @@ for the JavaScript code in this tag.
-
-

1.7 Template for HDF5 has/read/write a single string attribute

+
+

1.7 Template for HDF5 has/read/write a single string attribute

trexio_exit_code
@@ -1020,7 +1020,7 @@ for the JavaScript code in this tag.

Author: TREX-CoE

-

Created: 2021-06-25 Fri 12:16

+

Created: 2021-07-15 Thu 12:45

Validate

diff --git a/templator_text.html b/templator_text.html index eba93dd..23350c1 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 @@ -311,26 +311,26 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 TEXT back end

+
+

1 TEXT back end

The "file" produced by the text back end is a directory with one @@ -361,8 +361,8 @@ The file is written when closed, or when the flush function is called.

-
-

1.1 Template for group-related structures in text back end

+
+

1.1 Template for group-related structures in text back end

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

1.2 Template for general structure in text back end

+
+

1.2 Template for general structure in text back end

typedef struct rdm_s {
@@ -407,8 +407,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.3 Initialize function (constant part)

+
+

1.3 Initialize function (constant part)

trexio_exit_code
@@ -509,8 +509,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.4 Deinitialize function (templated part)

+
+

1.4 Deinitialize function (templated part)

trexio_exit_code
@@ -535,8 +535,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.5 Template for text read struct

+
+

1.5 Template for text read struct

$group$_t*
@@ -807,8 +807,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

1.6 Template for text flush struct

+
+

1.6 Template for text flush struct

trexio_exit_code
@@ -872,8 +872,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

1.7 Template for text free memory

+
+

1.7 Template for text free memory

Memory is allocated when reading. The following function frees memory. @@ -918,8 +918,8 @@ Memory is allocated when reading. The following function frees memory.

-
-

1.8 Template for has/read/write the num attribute

+
+

1.8 Template for has/read/write the num attribute

trexio_exit_code
@@ -981,8 +981,8 @@ Memory is allocated when reading. The following function frees memory.
-
-

1.9 Template for has/read/write the dataset of numerical data

+
+

1.9 Template for has/read/write the dataset of numerical data

The group_dset array is assumed allocated with the appropriate size. @@ -1078,8 +1078,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

1.10 Template for has/read/write the dataset of strings

+
+

1.10 Template for has/read/write the dataset of strings

The group_dset array is assumed allocated with the appropriate size. @@ -1181,8 +1181,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

1.11 Template for has/read/write the string attribute

+
+

1.11 Template for has/read/write the string attribute

trexio_exit_code
@@ -1256,12 +1256,12 @@ The group_dset array is assumed allocated with the appropriate size
-
-

1.12 RDM struct (hard-coded)

+
+

1.12 RDM struct (hard-coded)

-
-

1.12.1 Read the complete struct

+
+

1.12.1 Read the complete struct

rdm_t* trexio_text_read_rdm(trexio_text_t* const file);
@@ -1356,8 +1356,8 @@ The group_dset array is assumed allocated with the appropriate size
-
-

1.12.2 Flush the complete struct

+
+

1.12.2 Flush the complete struct

trexio_exit_code trexio_text_flush_rdm(trexio_text_t* const file);
@@ -1399,8 +1399,8 @@ The group_dset array is assumed allocated with the appropriate size
-
-

1.12.3 Free memory

+
+

1.12.3 Free memory

Memory is allocated when reading. The followig function frees memory. @@ -1436,8 +1436,8 @@ Memory is allocated when reading. The followig function frees memory.

-
-

1.12.4 Read/Write the onee attribute

+
+

1.12.4 Read/Write the onee attribute

The one_e array is assumed allocated with the appropriate size. @@ -1503,8 +1503,8 @@ The one_e array is assumed allocated with the appropriate size.

-
-

1.12.5 Read/Write the twoe attribute

+
+

1.12.5 Read/Write the twoe attribute

two_e is a sparse data structure, which can be too large to fit @@ -1612,7 +1612,7 @@ file for each sparse float structure.

Author: TREX-CoE

-

Created: 2021-06-25 Fri 12:16

+

Created: 2021-07-15 Thu 12:45

Validate

diff --git a/trex.html b/trex.html index e73b8cb..181675b 100644 --- a/trex.html +++ b/trex.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREX Configuration file @@ -333,28 +333,28 @@ for the JavaScript code in this tag.

Table of Contents

@@ -386,8 +386,8 @@ arrays are 0-based. Hence, we introduce the index type which is an 1-based int in the Fortran interface and 0-based otherwise.

-
-

1 Metadata (metadata group)

+
+

1 Metadata (metadata group)

As we expect our files to be archived in open-data repositories, we @@ -397,7 +397,7 @@ which have participated to the creation of the file, a list of authors of the file, and a textual description.

- +
@@ -457,15 +457,15 @@ authors of the file, and a textual description. -
-

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.

-
+
@@ -504,15 +504,15 @@ 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.

-
+
@@ -572,8 +572,8 @@ given in Cartesian \((x,y,z)\) format. -
-

4 TODO Effective core potentials (ecp group)

+
+

4 TODO Effective core potentials (ecp group)

An effective core potential (ECP) \(V_A^{\text{pp}}\) replacing the @@ -618,7 +618,7 @@ letters are parameters.

  • \(\hat{V}_\text{ecp,nl} = \sum_A \hat{V}_A^{\text{nl}}\) : non-local component
    • -
    +
    @@ -727,8 +727,8 @@ letters are parameters. -
    -

    5 Basis set (basis group)

    +
    +

    5 Basis set (basis group)

    We consider here basis functions centered on nuclei. Hence, we enable @@ -781,7 +781,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\). All the basis set parameters are stored in one-dimensional arrays:

    -
    +
    @@ -950,8 +950,8 @@ prim_factor = -
    -

    6 Atomic orbitals (ao group)

    +
    +

    6 Atomic orbitals (ao group)

    Going from the atomic basis set to AOs implies a systematic @@ -999,13 +999,13 @@ 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 \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).

    -
    +
    @@ -1057,8 +1057,8 @@ 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}} @@ -1076,7 +1076,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are over atomic orbitals.

      - +
      @@ -1143,8 +1143,8 @@ 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 @@ -1165,7 +1165,7 @@ notation. \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential -

      +
      @@ -1205,10 +1205,10 @@ notation. -
      -

      7 Molecular orbitals (mo group)

      +
      +

      7 Molecular orbitals (mo group)

      -
      +
      @@ -1274,8 +1274,8 @@ 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 @@ -1283,7 +1283,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

    - +
    @@ -1350,8 +1350,8 @@ 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 @@ -1359,7 +1359,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

    -
    +
    @@ -1399,13 +1399,13 @@ the basis of molecular orbitals. -
    -

    8 TODO Slater determinants

    +
    +

    8 TODO Slater determinants

    -
    -

    9 TODO Reduced density matrices (rdm group)

    +
    +

    9 TODO Reduced density matrices (rdm group)

    -
    +
    @@ -1458,15 +1458,15 @@ the basis of molecular orbitals. -
    -

    10 Appendix

    +
    +

    10 Appendix

    -
    -

    10.1 Python script from table to json

    +
    +

    10.1 Python script from table to json

    -
    print("""#+begin_src python :tangle trex.json""")
+
    print("""#+begin_src python :tangle trex.json""")
 print("""    "%s": {"""%(title))
 indent = "        "
 f1 = 0 ; f2 = 0 ; f3 = 0
@@ -1519,7 +1519,7 @@ the basis of molecular orbitals.

    Author: TREX-CoE

    -

    Created: 2021-06-25 Fri 12:16

    +

    Created: 2021-07-15 Thu 12:45

    Validate