diff --git a/README.html b/README.html index 2b5d27d..f4aadec 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: 2022-01-21 Fri 11:33

+

Created: 2022-01-24 Mon 17:22

Validate

diff --git a/examples.html b/examples.html index 58466b7..082ee51 100644 --- a/examples.html +++ b/examples.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Examples @@ -333,24 +333,24 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Accessing sparse quantities

+
+

1 Accessing sparse quantities

-
-

1.1 Fortran

+
+

1.1 Fortran

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

1.1.1 Declare Temporary variables

+
+

1.1.1 Declare Temporary variables

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

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

+
+

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

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

1.1.3 Read the nuclear repulsion energy

+
+

1.1.3 Read the nuclear repulsion energy

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

1.1.4 Read the number of molecular orbitals

+
+

1.1.4 Read the number of molecular orbitals

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

1.1.5 Allocate memory

+
+

1.1.5 Allocate memory

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

1.1.6 Read one-electron quantities

+
+

1.1.6 Read one-electron quantities

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

1.1.7 Read two-electron quantities

+
+

1.1.7 Read two-electron quantities

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

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

1.1.8 Compute the energy

+
+

1.1.8 Compute the energy

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

-
-

1.1.9 Terminate

+
+

1.1.9 Terminate

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

Author: TREX-CoE

-

Created: 2022-01-21 Fri 11:33

+

Created: 2022-01-24 Mon 17:22

Validate

diff --git a/index.html b/index.html index 2b5d27d..f4aadec 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: 2022-01-21 Fri 11:33

+

Created: 2022-01-24 Mon 17:22

Validate

diff --git a/templator_front.html b/templator_front.html index aa7b04f..58539b6 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 @@ -333,144 +333,151 @@ 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
    • @@ -485,8 +492,8 @@ 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 @@ -521,8 +528,8 @@ The maximum string size for the filenames is 4096 characters.

-
-

2 Front end

+
+

2 Front end

All calls to TREXIO are thread-safe. @@ -530,10 +537,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.

-
-

2.1 Error handling

+
+

2.1 Error handling

- +
@@ -774,8 +781,8 @@ 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 @@ -801,8 +808,8 @@ 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*
@@ -913,8 +920,8 @@ and the corresponding message are not propagated to the source code.
-
-
2.1.1.2 Fortran interface
+
+
2.1.1.2 Fortran interface
interface
@@ -930,8 +937,8 @@ 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):
@@ -970,8 +977,8 @@ and the corresponding message are not propagated to the source code.
-
-

2.2 Back ends

+
+

2.2 Back ends

TREXIO has several back ends: @@ -995,8 +1002,8 @@ 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;
@@ -1044,8 +1051,8 @@ 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
@@ -1085,8 +1092,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
-

2.2.3 Python

+
+

2.2.3 Python

# define TREXIO back ends
@@ -1100,8 +1107,8 @@ 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 @@ -1129,8 +1136,8 @@ 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 @@ -1164,8 +1171,8 @@ TREXIO files will have as a first argument the TREXIO file handle.

-
-

2.4.1 TREXIOFile Python class

+
+

2.4.1 TREXIOFile Python class

class File:
@@ -1247,8 +1254,8 @@ 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 @@ -1267,8 +1274,8 @@ 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. @@ -1307,8 +1314,8 @@ renaming the .txt data files.

-
-

2.6.1 C

+
+

2.6.1 C

trexio_t*
@@ -1495,8 +1502,8 @@ renaming the .txt data files.
-
-

2.6.2 Fortran

+
+

2.6.2 Fortran

interface
@@ -1514,8 +1521,8 @@ renaming the .txt data files.
-
-

2.6.3 Python

+
+

2.6.3 Python

def _open(file_name: str, mode: str, back_end: int):
@@ -1563,8 +1570,8 @@ renaming the .txt data files.
-
-

2.6.4 Zero-based versus one-based arrays of indices

+
+

2.6.4 Zero-based versus one-based arrays of indices

Because arrays are zero-based in Fortran, we need to set a flag to @@ -1598,8 +1605,8 @@ 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. @@ -1616,8 +1623,8 @@ output:

-
-

2.7.1 C

+
+

2.7.1 C

trexio_exit_code
@@ -1698,8 +1705,8 @@ output:
-
-

2.7.2 Fortran

+
+

2.7.2 Fortran

interface
@@ -1714,8 +1721,8 @@ output:
-
-

2.7.3 Python

+
+

2.7.3 Python

def _close(trexio_file):
@@ -1736,8 +1743,8 @@ output:
-
-

2.8 File existence

+
+

2.8 File existence

trexio_inquire check whether TREXIO file exists. @@ -1752,10 +1759,30 @@ input parameters: output: trexio_exit_code exit code.

+ +

+It returns: +

+ +
    +
  • TREXIO_SUCCESS if the file_name exists and if it correspond to a valid TREXIO file (i.e. a directory OR an HDF5 file)
    • +
  • TREXIO_FILE_ERROR if file_name exists but it is not a TREXIO file
    • +
  • TREXIO_FAILURE otherwise
    • +
+ +

+Also, there is an implicit way to have the aforementioned functionality. +Attempt to open a non-existing file with trexio_open function will result in a TREXIO_OPEN_ERROR exit code +(see the modified value that has been passed as a 4-th argument to trexio_open). +

+ +

+You can see examples of both functionalities in test_f.f90 (search for calls with _void suffix). +

-
-

2.8.1 C

+
+

2.8.1 C

trexio_exit_code
@@ -1785,8 +1812,8 @@ output:
-
-

2.8.2 Fortran

+
+

2.8.2 Fortran

The function below is a C binding. @@ -1806,8 +1833,8 @@ 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:
@@ -1827,12 +1854,12 @@ The front end Fortran function for trexio_inquire can be found in t
-
-

3 Templates for front end

+
+

3 Templates for front end

-
-

3.1 Description

+
+

3.1 Description

Consider the following block of trex.json: @@ -2053,12 +2080,12 @@ value will result in TREXIO_INVALID_ARG_2 exit code.

-
-

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

+
+

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

-
-

3.2.1 Introduction

+
+

3.2.1 Introduction

This section concerns API calls related to numerical attributes, @@ -2129,8 +2156,8 @@ namely single value of int/float types.

-
-

3.2.2 C templates for front end

+
+

3.2.2 C templates for front end

The C templates that correspond to each of the abovementioned @@ -2144,18 +2171,19 @@ precision (see Table above).

-
-
3.2.2.1 Function declarations
+
+
3.2.2.1 Function declarations
-
-
3.2.2.2 Source code for double precision functions
+
+
3.2.2.2 Source code for double precision functions
trexio_exit_code
 trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* const num)
 {
   if (file == NULL) return TREXIO_INVALID_ARG_1;
+  if (num  == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
 
   switch (file->back_end) {
@@ -2212,14 +2240,15 @@ precision (see Table above).
-
-
3.2.2.3 Source code for single precision functions
+
+
3.2.2.3 Source code for single precision functions
trexio_exit_code
 trexio_read_$group_num$_32 (trexio_t* const file, $group_num_dtype_single$* const num)
 {
   if (file == NULL) return TREXIO_INVALID_ARG_1;
+  if (num  == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
 
   $group_num_dtype_double$ num_64 = 0;
@@ -2288,8 +2317,8 @@ precision (see Table above).
-
-
3.2.2.4 Source code for default functions
+
+
3.2.2.4 Source code for default functions
trexio_exit_code
@@ -2344,8 +2373,8 @@ precision (see Table above).
-
-

3.2.3 Fortran templates for front end

+
+

3.2.3 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -2437,8 +2466,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.2.4 Python templates for front end

+
+

3.2.4 Python templates for front end

def write_$group_num$(trexio_file, num_w: $group_num_py_dtype$) -> None:
@@ -2523,12 +2552,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

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

+
+

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

-
-

3.3.1 Introduction

+
+

3.3.1 Introduction

This section concerns API calls related to datasets. @@ -2610,8 +2639,8 @@ This section concerns API calls related to datasets.

-
-

3.3.2 C templates for front end

+
+

3.3.2 C templates for front end

The C templates that correspond to each of the abovementioned functions can be found below. @@ -2622,12 +2651,12 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble

-
-
3.3.2.1 Function declarations
+
+
3.3.2.1 Function declarations
-
-
3.3.2.2 Source code for double precision functions
+
+
3.3.2.2 Source code for double precision functions
trexio_exit_code
@@ -2790,8 +2819,8 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
-
3.3.2.3 Source code for single precision functions
+
+
3.3.2.3 Source code for single precision functions
trexio_exit_code
@@ -2942,11 +2971,11 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
-
3.3.2.4 Source code for memory-safe functions
+
+
3.3.2.4 Source code for memory-safe functions
-
trexio_exit_code rc;
+
trexio_exit_code rc;
 int64_t $group_dset_dim$ = 0;
 
 /* Error handling for this call is added by the generator */
@@ -3102,8 +3131,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
-
-
3.3.2.5 Source code for default functions
+
+
3.3.2.5 Source code for default functions
trexio_exit_code
@@ -3178,8 +3207,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
-
-

3.3.3 Fortran templates for front end

+
+

3.3.3 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -3271,8 +3300,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.3.4 Python templates for front end

+
+

3.3.4 Python templates for front end

def write_$group_dset$(trexio_file, dset_w) -> None:
@@ -3467,12 +3496,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

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

+
+

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

-
-

3.4.1 Introduction

+
+

3.4.1 Introduction

Sparse data structures are used typically for large tensors such as @@ -3633,16 +3662,16 @@ This section concerns API calls related to sparse data structures.

-
-

3.4.2 C templates for front end

+
+

3.4.2 C templates for front end

-
-
3.4.2.1 Function declarations
+
+
3.4.2.1 Function declarations
-
-
3.4.2.2 Source code for default functions
+
+
3.4.2.2 Source code for default functions
trexio_exit_code trexio_read_safe_$group_dset$(trexio_t* const file,
@@ -3736,6 +3765,7 @@ This section concerns API calls related to sparse data structures.
 trexio_read_$group_dset$_size(trexio_t* const file, int64_t* const size_max)
 {
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
+  if (size_max == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
 
   switch (file->back_end) {
@@ -3917,8 +3947,8 @@ This section concerns API calls related to sparse data structures.
-
-

3.4.3 Fortran templates for front end

+
+

3.4.3 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -4019,8 +4049,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.4.4 Python templates for front end

+
+

3.4.4 Python templates for front end

def write_$group_dset$(trexio_file: File, offset_file: int, buffer_size: int, indices: list, values: list) -> None:
@@ -4241,12 +4271,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

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

+
+

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

-
-

3.5.1 Introduction

+
+

3.5.1 Introduction

This section concerns API calls related to datasets of strings. @@ -4286,8 +4316,8 @@ 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 @@ -4295,12 +4325,12 @@ to/from the TREXIO file (except for trexio_has_ functi

-
-
3.5.2.1 Function declarations
+
+
3.5.2.1 Function declarations
-
-
3.5.2.2 Source code for default functions
+
+
3.5.2.2 Source code for default functions
trexio_exit_code
@@ -4550,8 +4580,8 @@ 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. @@ -4650,8 +4680,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.5.4 Python templates for front end

+
+

3.5.4 Python templates for front end

def write_$group_dset$(trexio_file, dset_w: list) -> None:
@@ -4767,12 +4797,12 @@ 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. @@ -4812,16 +4842,16 @@ This section concerns API calls related to string attributes.

-
-

3.6.2 C templates for front end

+
+

3.6.2 C templates for front end

-
-
3.6.2.1 Function declarations
+
+
3.6.2.1 Function declarations
-
-
3.6.2.2 Source code for default functions
+
+
3.6.2.2 Source code for default functions
trexio_exit_code
@@ -4925,8 +4955,8 @@ 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. @@ -5006,8 +5036,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.6.4 Python templates for front end

+
+

3.6.4 Python templates for front end

def write_$group_str$(trexio_file, str_w: str) -> None:
@@ -5097,10 +5127,91 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

4 Fortran helper/wrapper functions

+
+

4 General helper functions

+This section contains general helper functions like trexio_info. +

+ +

+trexio_info prints information about the TREXIO configuration (see config.h file). +In particular: +

+ +
    +
  1. TREXIO_PACKAGE_VERSION [string]
    2. +
  2. HAVE_HDF5 [bool]
    3. +
  3. HDF5_VERSION [string] (optional, only if HAVE_HDF5 is true)
    4. +
  4. TREXIO_GIT_HASH [string]
    5. +
+
+ +
+

4.1 C

+
+
+
trexio_exit_code
+trexio_info (void)
+{
+  printf("TREXIO_PACKAGE_VERSION : %s\n", TREXIO_PACKAGE_VERSION);
+
+#ifdef TREXIO_GIT_HASH
+  printf("TREXIO_GIT_HASH        : %s\n", TREXIO_GIT_HASH);
+#else
+  printf("GIT_HASH is stored in the config.h file, which is missing.");
+#endif
+
+#ifdef HAVE_HDF5
+  printf("HAVE_HDF5              : true\n");
+  printf("%s\n", H5_VERS_INFO);
+#else
+  printf("HAVE_HDF5              : false\n");
+  printf("TREXIO configured without the HDF5 library\n");
+#endif
+
+  return TREXIO_SUCCESS;
+}
+
+
+
+
+ +
+

4.2 Fortran

+
+
+
interface
+   integer function trexio_info () bind(C)
+     use, intrinsic :: iso_c_binding
+   end function trexio_info
+end interface
+
+
+
+
+ +
+

4.3 Python

+
+
+
def info():
+    """Print the info about the installed TREXIO library.
+    """
+
+    rc = pytr.trexio_info()
+    if rc != TREXIO_SUCCESS:
+        raise Error(rc)
+
+
+
+
+
+ +
+

5 Fortran helper/wrapper functions

+
+

The function below adapts the original C-based trexio_open for Fortran. This is needed due to the fact that strings in C are terminated by NULL character \0 unlike strings in Fortran. @@ -5250,7 +5361,7 @@ two code are identical, i.e. if the assert statement pass.

Author: TREX-CoE

-

Created: 2022-01-21 Fri 11:33

+

Created: 2022-01-24 Mon 17:22

Validate

diff --git a/templator_hdf5.html b/templator_hdf5.html index 06aca5e..c4d6a29 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 @@ -311,29 +311,29 @@ 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          "$group$"
@@ -345,8 +345,8 @@ 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
@@ -460,8 +460,8 @@ for the JavaScript code in this tag.
-
-

1.4 Template for HDF5 has/read/write the numerical attribute

+
+

1.4 Template for HDF5 has/read/write the numerical attribute

trexio_exit_code
@@ -555,8 +555,8 @@ for the JavaScript code in this tag.
-
-

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

+
+

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

trexio_exit_code
@@ -678,8 +678,8 @@ for the JavaScript code in this tag.
-
-

1.6 Template for HDF5 has/read/write the dataset of sparse data

+
+

1.6 Template for HDF5 has/read/write the dataset of sparse data

Sparse data is stored using extensible datasets of HDF5. Extensibility is required @@ -880,8 +880,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s

-
-

1.7 Template for HDF5 has/read/write the dataset of strings

+
+

1.7 Template for HDF5 has/read/write the dataset of strings

trexio_exit_code
@@ -1085,8 +1085,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
-

1.8 Template for HDF5 has/read/write the string attribute

+
+

1.8 Template for HDF5 has/read/write the string attribute

trexio_exit_code
@@ -1208,8 +1208,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
-

1.9 Helper functions

+
+

1.9 Helper functions

trexio_exit_code
@@ -1471,7 +1471,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s

Author: TREX-CoE

-

Created: 2022-01-21 Fri 11:33

+

Created: 2022-01-24 Mon 17:22

Validate

diff --git a/templator_text.html b/templator_text.html index 51234c9..2100344 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 @@ -311,28 +311,28 @@ 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 @@ -353,8 +353,8 @@ 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 {
@@ -373,8 +373,8 @@ 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 trexio_text_s {
@@ -387,8 +387,8 @@ 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
@@ -531,8 +531,8 @@ 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
@@ -554,8 +554,8 @@ 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*
@@ -847,8 +847,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

1.6 Template for text flush struct

+
+

1.6 Template for text flush struct

trexio_exit_code
@@ -913,8 +913,8 @@ 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. @@ -959,8 +959,8 @@ Memory is allocated when reading. The following function frees memory.

-
-

1.8 Template for has/read/write the numerical attribute

+
+

1.8 Template for has/read/write the numerical attribute

trexio_exit_code
@@ -1023,8 +1023,8 @@ 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. @@ -1120,8 +1120,8 @@ 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. @@ -1222,8 +1222,8 @@ 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
@@ -1297,8 +1297,8 @@ The group_dset array is assumed allocated with the appropriate size
-
-

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

+
+

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

Each sparse array is stored in a separate .txt file due to the fact that sparse I/O has to be decoupled @@ -1575,7 +1575,7 @@ User provides indices and values of the sparse array as two separate variables.

Author: TREX-CoE

-

Created: 2022-01-21 Fri 11:33

+

Created: 2022-01-24 Mon 17:22

Validate

diff --git a/trex.html b/trex.html index ad8d308..b96a23b 100644 --- a/trex.html +++ b/trex.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREX Configuration file @@ -333,33 +333,33 @@ for the JavaScript code in this tag.

Table of Contents

@@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.

-
-

1 Metadata (metadata group)

+
+

1 Metadata (metadata group)

As we expect our files to be archived in open-data repositories, we @@ -420,7 +420,7 @@ which have participated to the creation of the file, a list of authors of the file, and a textual description.

-
+
@@ -487,15 +487,15 @@ 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.

-
+
@@ -534,15 +534,15 @@ 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.

-
+
@@ -609,8 +609,8 @@ 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 @@ -643,7 +643,7 @@ 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.

-
+
@@ -741,8 +741,8 @@ The latter causes issues when written before ang_mom in the TREXIO

-
-

4.1 Example

+
+

4.1 Example

For example, consider H2 molecule with the following @@ -805,8 +805,8 @@ power = [

-
-

5 Basis set (basis group)

+
+

5 Basis set (basis group)

We consider here basis functions centered on nuclei. Hence, we enable @@ -859,7 +859,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\). All the basis set parameters are stored in one-dimensional arrays:

-
+
@@ -953,8 +953,8 @@ 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 @@ -1032,8 +1032,8 @@ prim_factor =

-
-

6 Atomic orbitals (ao group)

+
+

6 Atomic orbitals (ao group)

Going from the atomic basis set to AOs implies a systematic @@ -1086,13 +1086,13 @@ 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 \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).

- +
@@ -1144,8 +1144,8 @@ 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}} @@ -1163,7 +1163,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are over atomic orbitals.

    - +
    @@ -1230,8 +1230,8 @@ 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 @@ -1252,7 +1252,7 @@ notation. \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential -

    +
    @@ -1292,10 +1292,10 @@ notation. -
    -

    7 Molecular orbitals (mo group)

    +
    +

    7 Molecular orbitals (mo group)

    -
    +
    @@ -1361,8 +1361,8 @@ 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 @@ -1370,7 +1370,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

- +
@@ -1437,8 +1437,8 @@ 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 @@ -1446,7 +1446,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

-
+
@@ -1486,11 +1486,11 @@ the basis of molecular orbitals. -
-

8 TODO Slater determinants

+
+

8 TODO Slater determinants

-
-

9 Reduced density matrices (rdm group)

+
+

9 Reduced density matrices (rdm group)

The reduced density matrices are defined in the basis of molecular @@ -1543,7 +1543,7 @@ The total energy can be computed as: \]

-
+
@@ -1626,7 +1626,7 @@ The total energy can be computed as:

Author: TREX-CoE

-

Created: 2022-01-21 Fri 11:33

+

Created: 2022-01-24 Mon 17:22

Validate