diff --git a/README.html b/README.html index ebb880e..c46c1b7 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: 2022-07-12 Tue 17:36

+

Created: 2022-07-26 Tue 12:07

Validate

diff --git a/examples.html b/examples.html index eff9701..72ca62c 100644 --- a/examples.html +++ b/examples.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Examples @@ -333,31 +333,31 @@ for the JavaScript code in this tag.

Table of Contents

@@ -365,12 +365,12 @@ for the JavaScript code in this tag.
-
-

1 Accessing sparse quantities (integrals)

+
+

1 Accessing sparse quantities (integrals)

-
-

1.1 Fortran

+
+

1.1 Fortran

program print_energy
@@ -416,8 +416,8 @@ 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
@@ -432,8 +432,8 @@ 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)
@@ -449,8 +449,8 @@ 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)
@@ -464,8 +464,8 @@ 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)
@@ -479,8 +479,8 @@ f = trexio_open (filename, 'r', TREXIO_HDF5
-
-

1.1.5 Allocate memory

+
+

1.1.5 Allocate memory

allocate( D(n,n), h0(n,n) )
@@ -492,8 +492,8 @@ 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)
@@ -525,8 +525,8 @@ 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 @@ -542,8 +542,8 @@ 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)
@@ -592,8 +592,8 @@ icount = BUFSIZE
-
-
1.1.7.2 Reduced density matrix
+
+
1.1.7.2 Reduced density matrix
rc = trexio_has_rdm_2e(f)
@@ -637,8 +637,8 @@ icount = bufsize
-
-

1.1.8 Compute the energy

+
+

1.1.8 Compute the energy

When the orbitals are real, we can use @@ -684,8 +684,8 @@ E = E + E_nn

-
-

1.1.9 Terminate

+
+

1.1.9 Terminate

  deallocate( D, h0, G, W )
@@ -699,12 +699,12 @@ E = E + E_nn
-
-

2 Reading determinants

+
+

2 Reading determinants

-
-

2.1 Fortran

+
+

2.1 Fortran

program test
@@ -783,7 +783,7 @@ end

Author: TREX-CoE

-

Created: 2022-07-12 Tue 17:36

+

Created: 2022-07-26 Tue 12:07

Validate

diff --git a/index.html b/index.html index ebb880e..c46c1b7 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: 2022-07-12 Tue 17:36

+

Created: 2022-07-26 Tue 12:07

Validate

diff --git a/templator_front.html b/templator_front.html index 08a766f..5db3b6a 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 @@ -333,186 +333,186 @@ 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
    • @@ -527,8 +527,8 @@ 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 @@ -564,8 +564,8 @@ The maximum string size for the filenames is 4096 characters.

-
-

2 Front end

+
+

2 Front end

All calls to TREXIO are thread-safe. @@ -573,10 +573,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.

-
-

2.1 Error handling

+
+

2.1 Error handling

- +
@@ -865,8 +865,8 @@ 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 @@ -892,8 +892,8 @@ 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*
@@ -1028,8 +1028,8 @@ and the corresponding message are not propagated to the source code.
-
-
2.1.1.2 Fortran interface
+
+
2.1.1.2 Fortran interface
interface
@@ -1045,8 +1045,8 @@ 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):
@@ -1079,8 +1079,8 @@ and the corresponding message are not propagated to the source code.
-
-

2.2 Back ends

+
+

2.2 Back ends

TREXIO has several back ends: @@ -1109,8 +1109,8 @@ 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;
@@ -1159,8 +1159,8 @@ 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
@@ -1201,8 +1201,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
-

2.2.3 Python

+
+

2.2.3 Python

# define TREXIO back ends
@@ -1217,8 +1217,8 @@ 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 @@ -1247,8 +1247,8 @@ 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 @@ -1404,8 +1404,8 @@ 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. @@ -1461,8 +1461,8 @@ renaming the .txt data files.

-
-

2.5.1 C

+
+

2.5.1 C

trexio_t*
@@ -1779,8 +1779,8 @@ renaming the .txt data files.
-
-

2.5.2 Fortran

+
+

2.5.2 Fortran

interface
@@ -1798,8 +1798,8 @@ renaming the .txt data files.
-
-

2.5.3 Python

+
+

2.5.3 Python

def _open(file_name: str, mode: str, back_end: int):
@@ -1847,8 +1847,8 @@ 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 @@ -1881,8 +1881,8 @@ 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. @@ -1899,8 +1899,8 @@ output:

-
-

2.6.1 C

+
+

2.6.1 C

trexio_exit_code
@@ -1985,8 +1985,8 @@ output:
-
-

2.6.2 Fortran

+
+

2.6.2 Fortran

interface
@@ -2001,8 +2001,8 @@ output:
-
-

2.6.3 Python

+
+

2.6.3 Python

def _close(trexio_file):
@@ -2020,8 +2020,8 @@ output:
-
-

2.7 File existence

+
+

2.7 File existence

trexio_inquire check whether TREXIO file exists. @@ -2058,8 +2058,8 @@ You can see examples of both functionalities in test_f.f90 (search

-
-

2.7.1 C

+
+

2.7.1 C

trexio_exit_code
@@ -2089,8 +2089,8 @@ You can see examples of both functionalities in test_f.f90  (search
-
-

2.7.2 Fortran

+
+

2.7.2 Fortran

The function below is a C binding. @@ -2110,8 +2110,8 @@ The front end Fortran function for trexio_inquire can be found in t

-
-

2.7.3 Python

+
+

2.7.3 Python

def _inquire(file_name: str) -> bool:
@@ -2130,8 +2130,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
-

2.8 File state

+
+

2.8 File state

trexio_set_state set an existing trexio_t file handle to a given state. @@ -2150,8 +2150,8 @@ output:

-
-

2.8.1 C

+
+

2.8.1 C

trexio_exit_code
@@ -2179,8 +2179,8 @@ output:
-
-

2.8.2 Fortran

+
+

2.8.2 Fortran

interface
@@ -2205,8 +2205,8 @@ output:
-
-

2.8.3 Python

+
+

2.8.3 Python

See TREXIO File Python class. @@ -2215,8 +2215,8 @@ See TREXIO File Python class.

-
-

2.9 Tasks to be done before closing

+
+

2.9 Tasks to be done before closing

trexio_exit_code
@@ -2317,12 +2317,12 @@ 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: @@ -2543,12 +2543,12 @@ 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 @@ -2578,8 +2578,8 @@ 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 @@ -2588,12 +2588,12 @@ 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
@@ -2630,8 +2630,8 @@ 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. @@ -2651,8 +2651,8 @@ 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:
@@ -2679,12 +2679,12 @@ 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, @@ -2755,8 +2755,8 @@ 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 @@ -2770,12 +2770,12 @@ 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
@@ -2839,8 +2839,8 @@ 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
@@ -2916,8 +2916,8 @@ 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
@@ -2972,8 +2972,8 @@ 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. @@ -3065,8 +3065,8 @@ 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:
@@ -3139,12 +3139,12 @@ 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. @@ -3226,8 +3226,8 @@ 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. @@ -3238,12 +3238,12 @@ 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
@@ -3406,8 +3406,8 @@ 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
@@ -3558,11 +3558,11 @@ 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 */
@@ -3718,8 +3718,8 @@ 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
@@ -3794,8 +3794,8 @@ 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. @@ -3887,8 +3887,8 @@ 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:
@@ -4060,12 +4060,12 @@ 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 @@ -4226,16 +4226,16 @@ 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,
@@ -4511,8 +4511,8 @@ 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. @@ -4613,8 +4613,8 @@ 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:
@@ -4816,12 +4816,12 @@ 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. @@ -4861,8 +4861,8 @@ 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 @@ -4870,12 +4870,12 @@ 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
@@ -5125,8 +5125,8 @@ 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. @@ -5225,8 +5225,8 @@ 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:
@@ -5327,12 +5327,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

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

+
+

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

-
-

3.7.1 Introduction

+
+

3.7.1 Introduction

This section concerns API calls related to string attributes. @@ -5372,16 +5372,16 @@ 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

-
-
3.7.2.1 Function declarations
+
+
3.7.2.1 Function declarations
-
-
3.7.2.2 Source code for default functions
+
+
3.7.2.2 Source code for default functions
trexio_exit_code
@@ -5485,8 +5485,8 @@ 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. @@ -5566,8 +5566,8 @@ 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 write_$group_str$(trexio_file, str_w: str) -> None:
@@ -5642,12 +5642,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

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

+
+

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

-
-

3.8.1 Introduction

+
+

3.8.1 Introduction

This section concerns API calls related to string attributes. @@ -5677,8 +5677,8 @@ 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

trexio_exit_code
@@ -5713,8 +5713,8 @@ 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. @@ -5734,8 +5734,8 @@ 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 delete_$group$(trexio_file) -> None:
@@ -5760,8 +5760,8 @@ 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, @@ -5832,8 +5832,8 @@ This section concerns API calls related to Slater determinants.

-
-

4.0.1 C source code

+
+

4.0.1 C source code

trexio_exit_code
@@ -6198,8 +6198,8 @@ 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. @@ -6356,8 +6356,8 @@ 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:
@@ -6681,8 +6681,8 @@ 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. @@ -6721,8 +6721,8 @@ into the corresponding int64_t bitfield representation of the deter

-
-

5.1 C

+
+

5.1 C

trexio_exit_code trexio_info(void);
@@ -6953,8 +6953,8 @@ into the corresponding int64_t bitfield representation of the deter
-
-

5.2 Fortran

+
+

5.2 Fortran

interface
@@ -7014,8 +7014,8 @@ into the corresponding int64_t bitfield representation of the deter
-
-

5.3 Python

+
+

5.3 Python

def info():
@@ -7122,8 +7122,8 @@ into the corresponding int64_t bitfield representation of the deter
-
-

6 Fortran helper/wrapper functions

+
+

6 Fortran helper/wrapper functions

The function below adapts the original C-based trexio_open for Fortran. @@ -7352,7 +7352,7 @@ two code are identical, i.e. if the assert statement pass.

Author: TREX-CoE

-

Created: 2022-07-12 Tue 17:36

+

Created: 2022-07-26 Tue 12:07

Validate

diff --git a/templator_hdf5.html b/templator_hdf5.html index de3c972..cf0f365 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 @@ -311,24 +311,24 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Template for HDF5 definitions

+
+

1 Template for HDF5 definitions

#define $GROUP$_GROUP_NAME          "$group$"
@@ -340,8 +340,8 @@ 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 @@ -361,8 +361,8 @@ 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
@@ -467,8 +467,8 @@ 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
@@ -498,8 +498,8 @@ 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
@@ -603,8 +603,8 @@ 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
@@ -738,8 +738,8 @@ 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 @@ -942,8 +942,8 @@ 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 strings

+
+

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

trexio_exit_code
@@ -1141,8 +1141,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
-

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

+
+

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

trexio_exit_code
@@ -1269,8 +1269,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
-

10 Template for HDF5 delete a group (UNSAFE mode)

+
+

10 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 @@ -1310,8 +1310,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of

-
-

11 Source code for the determinant part

+
+

11 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. @@ -1564,8 +1564,8 @@ Size specifies the number of data items (e.g. determinants) to process.

-
-

12 Helper functions

+
+

12 Helper functions

trexio_exit_code
@@ -1828,7 +1828,7 @@ Size specifies the number of data items (e.g. determinants) to process.

Author: TREX-CoE

-

Created: 2022-07-12 Tue 17:36

+

Created: 2022-07-26 Tue 12:07

Validate

diff --git a/templator_text.html b/templator_text.html index f7d8113..68fd986 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 @@ -311,21 +311,21 @@ for the JavaScript code in this tag.

Table of Contents

@@ -347,8 +347,8 @@ 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 {
@@ -367,8 +367,8 @@ 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 @@ -388,8 +388,8 @@ corresponding types for all back ends can be safely casted to

-
-

3 Initialize function (constant part)

+
+

3 Initialize function (constant part)

bool
@@ -556,8 +556,8 @@ corresponding types for all back ends can be safely casted to
-
-

4 Deinitialize function (templated part)

+
+

4 Deinitialize function (templated part)

trexio_exit_code
@@ -579,8 +579,8 @@ corresponding types for all back ends can be safely casted to
-
-

5 Template for text read a group

+
+

5 Template for text read a group

$group$_t*
@@ -806,8 +806,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

6 Template for text has a group

+
+

6 Template for text has a group

trexio_exit_code
@@ -847,8 +847,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

7 Template for text flush a group

+
+

7 Template for text flush a group

trexio_exit_code
@@ -912,8 +912,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

8 Template for text free memory

+
+

8 Template for text free memory

Memory is allocated when reading. The following function frees memory. @@ -982,8 +982,8 @@ This function is called upon the non-successful exit from the trexio_text_

-
-

9 Template for has/read/write a numerical attribute

+
+

9 Template for has/read/write a numerical attribute

trexio_exit_code
@@ -1046,8 +1046,8 @@ This function is called upon the non-successful exit from the trexio_text_
-
-

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

+
+

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

The group_dset array is assumed allocated with the appropriate size. @@ -1143,8 +1143,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

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

+
+

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

The group_dset array is assumed allocated with the appropriate size. @@ -1245,8 +1245,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

12 Template for has/read/write a string attribute

+
+

12 Template for has/read/write a string attribute

trexio_exit_code
@@ -1320,8 +1320,8 @@ The group_dset array is assumed allocated with the appropriate size
-
-

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

+
+

13 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 @@ -1611,8 +1611,8 @@ User provides indices and values of the sparse array as two separate variables.

-
-

14 Template for text delete a group (UNSAFE mode)

+
+

14 Template for text delete a group (UNSAFE mode)

trexio_exit_code
@@ -1640,8 +1640,8 @@ User provides indices and values of the sparse array as two separate variables.
-
-

15 Source code for the determinant part

+
+

15 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 @@ -2081,7 +2081,7 @@ Size specifies the number of data items, e.g. determinants.

Author: TREX-CoE

-

Created: 2022-07-12 Tue 17:36

+

Created: 2022-07-26 Tue 12:07

Validate

diff --git a/trex.html b/trex.html index 1ea1a84..e637de8 100644 --- a/trex.html +++ b/trex.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREX Configuration file @@ -333,37 +333,37 @@ for the JavaScript code in this tag.

Table of Contents

@@ -417,8 +417,8 @@ For determinants, the special attribute is present in the type. Thi means that the source code is not produced by the generator, but hand-written.

-
-

1 Metadata (metadata group)

+
+

1 Metadata (metadata group)

As we expect our files to be archived in open-data repositories, we @@ -428,7 +428,7 @@ which have participated to the creation of the file, a list of authors of the file, and a textual description.

- +
@@ -509,15 +509,15 @@ 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.

-
+
@@ -563,15 +563,15 @@ 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.

-
+
@@ -638,8 +638,8 @@ 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 @@ -672,7 +672,7 @@ 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.

-
+
@@ -774,8 +774,8 @@ 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 @@ -838,8 +838,8 @@ power = [

-
-

5 Basis set (basis group)

+
+

5 Basis set (basis group)

We consider here basis functions centered on nuclei. Hence, we enable @@ -892,7 +892,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\). All the basis set parameters are stored in one-dimensional arrays:

-
+
@@ -986,8 +986,8 @@ 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 @@ -1065,8 +1065,8 @@ prim_factor =

-
-

6 Atomic orbitals (ao group)

+
+

6 Atomic orbitals (ao group)

Going from the atomic basis set to AOs implies a systematic @@ -1119,13 +1119,13 @@ 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 \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).

- +
@@ -1177,8 +1177,8 @@ 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}} @@ -1195,7 +1195,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are over atomic orbitals.

    - +
    @@ -1290,8 +1290,8 @@ 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 @@ -1312,7 +1312,7 @@ notation. \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential -

    +
    @@ -1352,10 +1352,10 @@ notation. -
    -

    7 Molecular orbitals (mo group)

    +
    +

    7 Molecular orbitals (mo group)

    -
    +
    @@ -1442,8 +1442,8 @@ 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 @@ -1451,7 +1451,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

- +
@@ -1546,8 +1546,8 @@ 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 @@ -1555,7 +1555,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

-
+
@@ -1595,8 +1595,8 @@ the basis of molecular orbitals. -
-

8 Slater determinants (determinant group)

+
+

8 Slater determinants (determinant group)

The configuration interaction (CI) wave function \(\Psi\) @@ -1638,7 +1638,7 @@ produced by the code generator. An illustration on how to read determinants is presented in the examples.

-
+
@@ -1684,8 +1684,8 @@ An illustration on how to read determinants is presented in the -

9 Excited states (state group)

+
+

9 Excited states (state group)

By default, the determinant group corresponds to the ground state. @@ -1694,7 +1694,7 @@ correspond to excited state wave functions for the same set of determinants. This is the goal of the present group

-
+
@@ -1733,8 +1733,8 @@ 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 @@ -1787,7 +1787,7 @@ The total energy can be computed as: \]

-
+
@@ -1868,10 +1868,10 @@ The total energy can be computed as: -
-

11 Cell (cell group)

+
+

11 Cell (cell group)

-
+
@@ -1917,10 +1917,10 @@ The total energy can be computed as: -
-

12 Periodic boundary calculations (pbc group)

+
+

12 Periodic boundary calculations (pbc group)

-
+
@@ -1959,8 +1959,8 @@ The total energy can be computed as: -
-

13 Quantum Monte Carlo data (qmc group)

+
+

13 Quantum Monte Carlo data (qmc group)

In quantum Monte Carlo calculations, the wave function is evaluated @@ -1974,7 +1974,7 @@ By convention, the electron coordinates contain first all the electrons of $↑$-spin and then all the $↓$-spin.

-
+
@@ -2029,7 +2029,7 @@ of $↑$-spin and then all the $↓$-spin.