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#+TITLE: Front end API
#+PROPERTY: comments org
#+SETUPFILE: ../../docs/theme.setup
# -*- mode: org -*-
* Constant file prefixes (not used by generator) :noexport:
Prefixes in C contain mainly ~#include~ as well as some
~#define~ and ~typedef~ statements.
Prefixes in Fortran contain back-end definitions.
#+NAME:header
#+begin_src c
/* This file was generated from the templator_front.org org-mode file.
To generate it, open templator_front.org in Emacs and execute
M-x org-babel-tangle
*/
#+end_src
** C
#+begin_src c :tangle prefix_front.h :noweb yes
<<header>>
#ifndef TREXIO_H
#define TREXIO_H
#include <stdbool.h>
#include <stdint.h>
typedef int32_t trexio_exit_code;
#+end_src
#+begin_src c :tangle prefix_front.c :noweb yes
<<header>>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <pthread.h>
#include <assert.h>
#include <stdlib.h>
#include <stdbool.h>
#include <string.h>
#include <err.h>
#include "trexio.h"
#include "trexio_private.h"
#include "trexio_s.h"
#include "trexio_text.h"
#ifdef HAVE_HDF5
#include "trexio_hdf5.h"
#endif
/*
#include "trexio_json.h"
,*/
#+end_src
#+begin_src c :tangle prefix_s_front.h :noweb yes
<<header>>
#ifndef _TREXIO_S_H
#define _TREXIO_S_H
#include "trexio.h"
#include "trexio_private.h"
#include <pthread.h>
#include <stdbool.h>
#+end_src
#+begin_src c :tangle trexio_private.h :noweb yes
<<header>>
#ifndef _TREXIO_PRIVATE_H
#define _TREXIO_PRIVATE_H
#include "trexio.h"
#+end_src
** Fortran
#+begin_src f90 :tangle prefix_fortran.f90
module trexio
use, intrinsic :: iso_c_binding
implicit none
integer, parameter :: trexio_exit_code = c_int32_t
integer, parameter :: trexio_back_end_t = c_int32_t
integer, parameter :: trexio_t = c_int64_t
character(kind=c_char), parameter :: TREXIO_DELIM = c_new_line
#+end_src
** Python
#+begin_src python :tangle prefix_python.py
"""The Python API of the TREXIO library.
This package is a top-level wrapper of the SWIG-generated pytrexio module.
"""
try:
import pytrexio.pytrexio as pytr
except ImportError:
raise Exception("Could not import pytrexio module from trexio package")
# define max length of a string to be read, required for the low-level C routines
PYTREXIO_MAX_STR_LENGTH = 2048
# setuptools do not assign __version__ variable to the trexio package, so we set it manually
from os import path
__trexio_path__ = path.dirname(path.abspath(__file__))
with open(path.join(path.join(__trexio_path__, 'pytrexio'), '_version.py')) as version_file:
__version__ = version_file.read().split('"')[1]
__trexio_path__ = None
#+end_src
* Coding conventions
- integer types will be defined using types given in ~stdint.h~
- pointers are always initialized to ~NULL~
- when memory is freed, the pointer is set to ~NULL~
- ~assert.h~ should be used extensively
- variable names are in lower case
- ~#define~ constants are in upper case
- structs are suffixed by ~_s~
- types are suffixed by ~_t~
- API calls return ~trexio_exit_code~ (except for ~trexio_open~ function)
** Memory allocation
Memory allocation of structures can be facilitated by using the
following macros, which ensure that the size of the allocated
object is the same as the size of the data type pointed by the pointer.
For CALLOC, we allocate N+1 to avoid errors when N=0.
#+begin_src c :tangle trexio_private.h
#define MALLOC(T) (T*) malloc (sizeof(T))
#define CALLOC(N,T) (T*) calloc ( (N)+1 , sizeof(T) )
#+end_src
When a pointer is freed, it should be set to ~NULL~.
This can be facilitated by the use of the following macro:
#+begin_src c :tangle trexio_private.h
#define FREE(X) { free(X) ; (X)=NULL; }
#+end_src
The maximum string size for the filenames is 4096 characters.
#+begin_src c :tangle trexio_private.h
#define TREXIO_MAX_FILENAME_LENGTH 4096
#+end_src
* Front end
All calls to TREXIO are thread-safe.
TREXIO front end is modular, which simplifies implementation of new back ends.
** Error handling
#+NAME: table-exit-codes
| Macro | Code | Description |
|----------------------------------+------+----------------------------------------|
| ~TREXIO_FAILURE~ | -1 | 'Unknown failure' |
| ~TREXIO_SUCCESS~ | 0 | 'Success' |
| ~TREXIO_INVALID_ARG_1~ | 1 | 'Invalid argument 1' |
| ~TREXIO_INVALID_ARG_2~ | 2 | 'Invalid argument 2' |
| ~TREXIO_INVALID_ARG_3~ | 3 | 'Invalid argument 3' |
| ~TREXIO_INVALID_ARG_4~ | 4 | 'Invalid argument 4' |
| ~TREXIO_INVALID_ARG_5~ | 5 | 'Invalid argument 5' |
| ~TREXIO_END~ | 6 | 'End of file' |
| ~TREXIO_READONLY~ | 7 | 'Read-only file' |
| ~TREXIO_ERRNO~ | 8 | strerror(errno) |
| ~TREXIO_INVALID_ID~ | 9 | 'Invalid ID' |
| ~TREXIO_ALLOCATION_FAILED~ | 10 | 'Allocation failed' |
| ~TREXIO_HAS_NOT~ | 11 | 'Element absent' |
| ~TREXIO_INVALID_NUM~ | 12 | 'Invalid (negative or 0) dimension' |
| ~TREXIO_ATTR_ALREADY_EXISTS~ | 13 | 'Attribute already exists' |
| ~TREXIO_DSET_ALREADY_EXISTS~ | 14 | 'Dataset already exists' |
| ~TREXIO_OPEN_ERROR~ | 15 | 'Error opening file' |
| ~TREXIO_LOCK_ERROR~ | 16 | 'Error locking file' |
| ~TREXIO_UNLOCK_ERROR~ | 17 | 'Error unlocking file' |
| ~TREXIO_FILE_ERROR~ | 18 | 'Invalid file' |
| ~TREXIO_GROUP_READ_ERROR~ | 19 | 'Error reading group' |
| ~TREXIO_GROUP_WRITE_ERROR~ | 20 | 'Error writing group' |
| ~TREXIO_ELEM_READ_ERROR~ | 21 | 'Error reading element' |
| ~TREXIO_ELEM_WRITE_ERROR~ | 22 | 'Error writing element' |
| ~TREXIO_UNSAFE_ARRAY_DIM~ | 23 | 'Access to memory beyond allocated' |
| ~TREXIO_ATTR_MISSING~ | 24 | 'Attribute does not exist in the file' |
| ~TREXIO_DSET_MISSING~ | 25 | 'Dataset does not exist in the file' |
| ~TREXIO_BACK_END_MISSING~ | 26 | 'Requested back end is disabled' |
| ~TREXIO_INVALID_ARG_6~ | 27 | 'Invalid argument 6' |
| ~TREXIO_INVALID_ARG_7~ | 28 | 'Invalid argument 7' |
| ~TREXIO_INVALID_ARG_8~ | 29 | 'Invalid argument 8' |
| ~TREXIO_INVALID_STR_LEN~ | 30 | 'Invalid max_str_len' |
| ~TREXIO_INT_SIZE_OVERFLOW~ | 31 | 'Possible integer overflow' |
| ~TREXIO_SAFE_MODE~ | 32 | 'Unsafe operation in safe mode' |
| ~TREXIO_INVALID_ELECTRON_NUM~ | 33 | 'Inconsistent number of electrons' |
| ~TREXIO_INVALID_DETERMINANT_NUM~ | 34 | 'Inconsistent number of determinants' |
| ~TREXIO_INVALID_STATE~ | 35 | 'Inconsistent state of the file' |
| ~TREXIO_VERSION_PARSING_ISSUE~ | 36 | 'Failed to parse package_version' |
# We need to force Emacs not to indent the Python code:
# -*- org-src-preserve-indentation: t
*IMPORTANT!*
The code below has to be executed within Emacs each time
a new error code is added to the table above. Otherwise, the codes
and the corresponding message are not propagated to the source code.
#+begin_src python :var table=table-exit-codes :results drawer
""" This script generates the C and Fortran constants for the error
codes from the org-mode table.
"""
result = [ "#+begin_src c :tangle prefix_front.h :exports none" ]
for (text, code,_) in table:
text=text.replace("~","")
result += [ f"#define {text:30s} ((trexio_exit_code) {code:d})" ]
result += [ "#+end_src" ]
result += [ "" ]
result += [ "#+begin_src f90 :tangle prefix_fortran.f90 :exports none" ]
for (text, code,_) in table:
text=text.replace("~","")
result += [ f" integer(trexio_exit_code), parameter :: {text:30s} = {code:d}" ]
result += [ "#+end_src" ]
result += [ "" ]
result += [ "#+begin_src python :tangle prefix_python.py :exports none" ]
result += [ "# define TREXIO exit codes" ]
for (text, code,_) in table:
text=text.replace("~","")
result += [ f"{text:30s} = {code:d}" ]
result += [ "#+end_src" ]
return '\n'.join(result)
#+end_src
#+RESULTS:
:RESULTS:
#+begin_src c :tangle prefix_front.h :exports none
#define TREXIO_FAILURE ((trexio_exit_code) -1)
#define TREXIO_SUCCESS ((trexio_exit_code) 0)
#define TREXIO_INVALID_ARG_1 ((trexio_exit_code) 1)
#define TREXIO_INVALID_ARG_2 ((trexio_exit_code) 2)
#define TREXIO_INVALID_ARG_3 ((trexio_exit_code) 3)
#define TREXIO_INVALID_ARG_4 ((trexio_exit_code) 4)
#define TREXIO_INVALID_ARG_5 ((trexio_exit_code) 5)
#define TREXIO_END ((trexio_exit_code) 6)
#define TREXIO_READONLY ((trexio_exit_code) 7)
#define TREXIO_ERRNO ((trexio_exit_code) 8)
#define TREXIO_INVALID_ID ((trexio_exit_code) 9)
#define TREXIO_ALLOCATION_FAILED ((trexio_exit_code) 10)
#define TREXIO_HAS_NOT ((trexio_exit_code) 11)
#define TREXIO_INVALID_NUM ((trexio_exit_code) 12)
#define TREXIO_ATTR_ALREADY_EXISTS ((trexio_exit_code) 13)
#define TREXIO_DSET_ALREADY_EXISTS ((trexio_exit_code) 14)
#define TREXIO_OPEN_ERROR ((trexio_exit_code) 15)
#define TREXIO_LOCK_ERROR ((trexio_exit_code) 16)
#define TREXIO_UNLOCK_ERROR ((trexio_exit_code) 17)
#define TREXIO_FILE_ERROR ((trexio_exit_code) 18)
#define TREXIO_GROUP_READ_ERROR ((trexio_exit_code) 19)
#define TREXIO_GROUP_WRITE_ERROR ((trexio_exit_code) 20)
#define TREXIO_ELEM_READ_ERROR ((trexio_exit_code) 21)
#define TREXIO_ELEM_WRITE_ERROR ((trexio_exit_code) 22)
#define TREXIO_UNSAFE_ARRAY_DIM ((trexio_exit_code) 23)
#define TREXIO_ATTR_MISSING ((trexio_exit_code) 24)
#define TREXIO_DSET_MISSING ((trexio_exit_code) 25)
#define TREXIO_BACK_END_MISSING ((trexio_exit_code) 26)
#define TREXIO_INVALID_ARG_6 ((trexio_exit_code) 27)
#define TREXIO_INVALID_ARG_7 ((trexio_exit_code) 28)
#define TREXIO_INVALID_ARG_8 ((trexio_exit_code) 29)
#define TREXIO_INVALID_STR_LEN ((trexio_exit_code) 30)
#define TREXIO_INT_SIZE_OVERFLOW ((trexio_exit_code) 31)
#define TREXIO_SAFE_MODE ((trexio_exit_code) 32)
#define TREXIO_INVALID_ELECTRON_NUM ((trexio_exit_code) 33)
#define TREXIO_INVALID_DETERMINANT_NUM ((trexio_exit_code) 34)
#define TREXIO_INVALID_STATE ((trexio_exit_code) 35)
#define TREXIO_VERSION_PARSING_ISSUE ((trexio_exit_code) 36)
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90 :exports none
integer(trexio_exit_code), parameter :: TREXIO_FAILURE = -1
integer(trexio_exit_code), parameter :: TREXIO_SUCCESS = 0
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_1 = 1
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_2 = 2
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_3 = 3
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_4 = 4
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_5 = 5
integer(trexio_exit_code), parameter :: TREXIO_END = 6
integer(trexio_exit_code), parameter :: TREXIO_READONLY = 7
integer(trexio_exit_code), parameter :: TREXIO_ERRNO = 8
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ID = 9
integer(trexio_exit_code), parameter :: TREXIO_ALLOCATION_FAILED = 10
integer(trexio_exit_code), parameter :: TREXIO_HAS_NOT = 11
integer(trexio_exit_code), parameter :: TREXIO_INVALID_NUM = 12
integer(trexio_exit_code), parameter :: TREXIO_ATTR_ALREADY_EXISTS = 13
integer(trexio_exit_code), parameter :: TREXIO_DSET_ALREADY_EXISTS = 14
integer(trexio_exit_code), parameter :: TREXIO_OPEN_ERROR = 15
integer(trexio_exit_code), parameter :: TREXIO_LOCK_ERROR = 16
integer(trexio_exit_code), parameter :: TREXIO_UNLOCK_ERROR = 17
integer(trexio_exit_code), parameter :: TREXIO_FILE_ERROR = 18
integer(trexio_exit_code), parameter :: TREXIO_GROUP_READ_ERROR = 19
integer(trexio_exit_code), parameter :: TREXIO_GROUP_WRITE_ERROR = 20
integer(trexio_exit_code), parameter :: TREXIO_ELEM_READ_ERROR = 21
integer(trexio_exit_code), parameter :: TREXIO_ELEM_WRITE_ERROR = 22
integer(trexio_exit_code), parameter :: TREXIO_UNSAFE_ARRAY_DIM = 23
integer(trexio_exit_code), parameter :: TREXIO_ATTR_MISSING = 24
integer(trexio_exit_code), parameter :: TREXIO_DSET_MISSING = 25
integer(trexio_exit_code), parameter :: TREXIO_BACK_END_MISSING = 26
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_6 = 27
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_7 = 28
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ARG_8 = 29
integer(trexio_exit_code), parameter :: TREXIO_INVALID_STR_LEN = 30
integer(trexio_exit_code), parameter :: TREXIO_INT_SIZE_OVERFLOW = 31
integer(trexio_exit_code), parameter :: TREXIO_SAFE_MODE = 32
integer(trexio_exit_code), parameter :: TREXIO_INVALID_ELECTRON_NUM = 33
integer(trexio_exit_code), parameter :: TREXIO_INVALID_DETERMINANT_NUM = 34
integer(trexio_exit_code), parameter :: TREXIO_INVALID_STATE = 35
integer(trexio_exit_code), parameter :: TREXIO_VERSION_PARSING_ISSUE = 36
#+end_src
#+begin_src python :tangle prefix_python.py :exports none
# define TREXIO exit codes
TREXIO_FAILURE = -1
TREXIO_SUCCESS = 0
TREXIO_INVALID_ARG_1 = 1
TREXIO_INVALID_ARG_2 = 2
TREXIO_INVALID_ARG_3 = 3
TREXIO_INVALID_ARG_4 = 4
TREXIO_INVALID_ARG_5 = 5
TREXIO_END = 6
TREXIO_READONLY = 7
TREXIO_ERRNO = 8
TREXIO_INVALID_ID = 9
TREXIO_ALLOCATION_FAILED = 10
TREXIO_HAS_NOT = 11
TREXIO_INVALID_NUM = 12
TREXIO_ATTR_ALREADY_EXISTS = 13
TREXIO_DSET_ALREADY_EXISTS = 14
TREXIO_OPEN_ERROR = 15
TREXIO_LOCK_ERROR = 16
TREXIO_UNLOCK_ERROR = 17
TREXIO_FILE_ERROR = 18
TREXIO_GROUP_READ_ERROR = 19
TREXIO_GROUP_WRITE_ERROR = 20
TREXIO_ELEM_READ_ERROR = 21
TREXIO_ELEM_WRITE_ERROR = 22
TREXIO_UNSAFE_ARRAY_DIM = 23
TREXIO_ATTR_MISSING = 24
TREXIO_DSET_MISSING = 25
TREXIO_BACK_END_MISSING = 26
TREXIO_INVALID_ARG_6 = 27
TREXIO_INVALID_ARG_7 = 28
TREXIO_INVALID_ARG_8 = 29
TREXIO_INVALID_STR_LEN = 30
TREXIO_INT_SIZE_OVERFLOW = 31
TREXIO_SAFE_MODE = 32
TREXIO_INVALID_ELECTRON_NUM = 33
TREXIO_INVALID_DETERMINANT_NUM = 34
TREXIO_INVALID_STATE = 35
TREXIO_VERSION_PARSING_ISSUE = 36
#+end_src
:END:
*** Decoding errors
The ~trexio_string_of_error~ converts an exit code into a string. The
string is assumed to be large enough to contain the error message
(typically 128 characters).
To decode the error messages, ~trexio_string_of_error~ converts an
error code into a string.
#+NAME: MAX_STRING_LENGTH
: 128
#+begin_src c :tangle prefix_front.h :exports none :noweb yes
const char* trexio_string_of_error(const trexio_exit_code error);
void trexio_string_of_error_f(const trexio_exit_code error, char result[<<MAX_STRING_LENGTH()>>]);
#+end_src
*IMPORTANT!*
The code below has to be executed within Emacs each time
a new error code is added to the table above. Otherwise, the codes
and the corresponding message are not propagated to the source code.
#+NAME:cases
#+begin_src python :var table=table-exit-codes :exports none :noweb yes
""" This script extracts the text associated with the error codes
from the table.
"""
result = []
for (text, code, message) in table:
text = text.replace("~","")
message = message.replace("'",'"')
result += [ f"""case {text}:\n return {message};\n break;""" ]
return '\n'.join(result)
#+end_src
#+RESULTS: cases
#+begin_example
case TREXIO_FAILURE:
return "Unknown failure";
break;
case TREXIO_SUCCESS:
return "Success";
break;
case TREXIO_INVALID_ARG_1:
return "Invalid argument 1";
break;
case TREXIO_INVALID_ARG_2:
return "Invalid argument 2";
break;
case TREXIO_INVALID_ARG_3:
return "Invalid argument 3";
break;
case TREXIO_INVALID_ARG_4:
return "Invalid argument 4";
break;
case TREXIO_INVALID_ARG_5:
return "Invalid argument 5";
break;
case TREXIO_END:
return "End of file";
break;
case TREXIO_READONLY:
return "Read-only file";
break;
case TREXIO_ERRNO:
return strerror(errno);
break;
case TREXIO_INVALID_ID:
return "Invalid ID";
break;
case TREXIO_ALLOCATION_FAILED:
return "Allocation failed";
break;
case TREXIO_HAS_NOT:
return "Element absent";
break;
case TREXIO_INVALID_NUM:
return "Invalid (negative or 0) dimension";
break;
case TREXIO_ATTR_ALREADY_EXISTS:
return "Attribute already exists";
break;
case TREXIO_DSET_ALREADY_EXISTS:
return "Dataset already exists";
break;
case TREXIO_OPEN_ERROR:
return "Error opening file";
break;
case TREXIO_LOCK_ERROR:
return "Error locking file";
break;
case TREXIO_UNLOCK_ERROR:
return "Error unlocking file";
break;
case TREXIO_FILE_ERROR:
return "Invalid file";
break;
case TREXIO_GROUP_READ_ERROR:
return "Error reading group";
break;
case TREXIO_GROUP_WRITE_ERROR:
return "Error writing group";
break;
case TREXIO_ELEM_READ_ERROR:
return "Error reading element";
break;
case TREXIO_ELEM_WRITE_ERROR:
return "Error writing element";
break;
case TREXIO_UNSAFE_ARRAY_DIM:
return "Access to memory beyond allocated";
break;
case TREXIO_ATTR_MISSING:
return "Attribute does not exist in the file";
break;
case TREXIO_DSET_MISSING:
return "Dataset does not exist in the file";
break;
case TREXIO_BACK_END_MISSING:
return "Requested back end is disabled";
break;
case TREXIO_INVALID_ARG_6:
return "Invalid argument 6";
break;
case TREXIO_INVALID_ARG_7:
return "Invalid argument 7";
break;
case TREXIO_INVALID_ARG_8:
return "Invalid argument 8";
break;
case TREXIO_INVALID_STR_LEN:
return "Invalid max_str_len";
break;
case TREXIO_INT_SIZE_OVERFLOW:
return "Possible integer overflow";
break;
case TREXIO_SAFE_MODE:
return "Unsafe operation in safe mode";
break;
case TREXIO_INVALID_ELECTRON_NUM:
return "Inconsistent number of electrons";
break;
case TREXIO_INVALID_DETERMINANT_NUM:
return "Inconsistent number of determinants";
break;
case TREXIO_INVALID_STATE:
return "Inconsistent state of the file";
break;
case TREXIO_VERSION_PARSING_ISSUE:
return "Failed to parse package_version";
break;
#+end_example
**** C source code
#+begin_src c :tangle prefix_front.c :noweb yes
const char*
trexio_string_of_error (const trexio_exit_code error)
{
switch (error) {
<<cases()>>
}
return "Unknown error";
}
void
trexio_string_of_error_f (const trexio_exit_code error, char result[<<MAX_STRING_LENGTH()>>])
{
strncpy(result, trexio_string_of_error(error), <<MAX_STRING_LENGTH()>>);
}
#+end_src
**** Fortran interface
#+begin_src f90 :tangle prefix_fortran.f90 :noexport :noweb yes
interface
subroutine trexio_string_of_error (error, string) bind(C, name='trexio_string_of_error_f')
use, intrinsic :: iso_c_binding
import
integer(trexio_exit_code), intent(in), value :: error
character(kind=c_char), intent(out) :: string(<<MAX_STRING_LENGTH()>>)
end subroutine trexio_string_of_error
end interface
#+end_src
**** Python interface
#+begin_src python :tangle prefix_python.py :noexport
class Error(Exception):
"""Base class for TREXIO errors.
Attributes:
error: int -- exit code returned by the call to TREXIO library;
message: str -- decoded string corresponding to trexio_exit_code.
"""
def __init__(self, trexio_return_code):
self.error = trexio_return_code
self.message = string_of_error(trexio_return_code)
super().__init__(self.message)
def string_of_error(return_code: int) -> str:
"""Decode the TREXIO exit code.
Argument is an integer return code that correspond to one of the TREXIO errors.
Returns a string that contains description of TREXIO ~return_code~.
"""
return pytr.trexio_string_of_error(return_code)
#+end_src
** Back ends
TREXIO has several back ends:
1) ~TREXIO_HDF5~ relies on extensive use of the HDF5 library and the associated file format. The HDF5 file is binary and tailored to high-performance I/O. This back end is the default one. HDF5 can be compiled with MPI for parallel I/O. Note, that HDF5 has to be downloaded and installed independently of TREXIO, which may cause some obstacles, especially when the user is not allowed to install external software. The produced files usually have ~.h5~ extension.
2) ~TREXIO_TEXT~ relies on basic file I/O in C, namely ~fopen, fclose, fprintf, fscanf~ etc. from ~stdio.h~ library. This back end is not optimized for performance. It is supposed to be used for debug purposes or, for example, when the user wants to modify some data manually within the file. This back end is supposed to work "out-of-the-box" since there are no external dependencies, which might be useful for users that do not have access to HDF5 library. The produced files usually have ~.txt~ extension.
~TREXIO_AUTO~ can be provided as a back end when opening an existing TREXIO file in read-only ~'r'~ mode.
In this case, TREXIO will try to automatically detect the back end, which should be used to open the file.
Additional back ends can be implemented thanks to the modular nature of the front end.
This can be achieved by adding a new ~case~ (corresponding to the desired back end) in the front-end ~switch~.
Then the corresponding back-end ~has/read/write~ functions has to be implemented. For example, see the commented
lines that correspond to the ~TREXIO_JSON~ back end (not implemented yet).
_Note_: It is important to increment the value of ~TREXIO_INVALID_BACK_END~ when a new back end is implemented. Otherwise, it will not be available.
*** C
#+begin_src c :tangle prefix_front.h
typedef int32_t back_end_t;
#define TREXIO_HDF5 ( (back_end_t) 0 )
#define TREXIO_TEXT ( (back_end_t) 1 )
#define TREXIO_INVALID_BACK_END ( (back_end_t) 2 )
#define TREXIO_AUTO TREXIO_INVALID_BACK_END
/*#define TREXIO_JSON ( (back_end_t) 2 )*/
#define TREXIO_DELIM "\n"
#+end_src
The helper function ~trexio_has_back_end~ returns ~true~ if TREXIO compilation includes a back end provided as an argument; ~false~ otherwise.
This is useful due to the fact that HDF5 back end can be disabled at configure step.
#+begin_src c :tangle prefix_front.h
bool trexio_has_backend(back_end_t back_end);
bool trexio_has_back_end(back_end_t back_end);
#+end_src
#+begin_src c :tangle prefix_front.c
bool trexio_has_back_end(back_end_t back_end) {
switch (back_end) {
case TREXIO_TEXT:
return true;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return true;
#else
return false;
#endif
}
return false;
}
bool trexio_has_backend(back_end_t back_end) {
return trexio_has_back_end(back_end);
}
#+end_src
*** Fortran
#+begin_src f90 :tangle prefix_fortran.f90
integer(trexio_back_end_t), parameter :: TREXIO_HDF5 = 0
integer(trexio_back_end_t), parameter :: TREXIO_TEXT = 1
! integer(trexio_back_end_t), parameter :: TREXIO_JSON = 2
integer(trexio_back_end_t), parameter :: TREXIO_INVALID_BACK_END = 2
integer(trexio_back_end_t), parameter :: TREXIO_AUTO = TREXIO_INVALID_BACK_END
#+end_src
The function below is a Fortran interface for the aforementioned C-compatible ~trexio_has_back_end~ function.
#+begin_src f90 :tangle prefix_fortran.f90
interface
logical(c_bool) function trexio_has_back_end (back_end) bind(C)
use, intrinsic :: iso_c_binding
import
integer(trexio_back_end_t), intent(in), value :: back_end
end function trexio_has_back_end
end interface
interface
logical(c_bool) function trexio_has_backend (back_end) bind(C)
use, intrinsic :: iso_c_binding
import
integer(trexio_back_end_t), intent(in), value :: back_end
end function trexio_has_backend
end interface
#+end_src
Originally, the function was named ~trexio_has_backend~. For
consistency, in version 2.2 it was renamed ~trexio_has_back_end~.
*** Python
#+begin_src python :tangle prefix_python.py
# define TREXIO back ends
TREXIO_HDF5 = 0
TREXIO_TEXT = 1
#TREXIO_JSON = 2
TREXIO_INVALID_BACK_END = 2
TREXIO_AUTO = TREXIO_INVALID_BACK_END
#+end_src
** Read/write behavior
Every time a reading function is called, the data is read from the
disk. If data needs to be cached, this is left to the user of the
library.
Writing to TREXIO files is done with transactions (all-or-nothing
effect). File writes are attempted by
calling explicitly the write (~TREXIO_HDF5~) or flush (~TREXIO_TEXT~)
function, or when the TREXIO file is closed.
If writing is impossible because the data is not valid, no data is written.
The order in which the data is written is not necessarily consistent
with the order in which the function calls were made.
The TREXIO files are supposed to be opened by only one program at a
time: if the same TREXIO file is modified simultaneously by multiple
concurrent programs, the behavior is not specified.
** TREXIO file type
~trexio_s~ is the the main type for TREXIO files, visible to the users
of the library. This type is kept opaque, and all modifications to
the files will be necessarily done through the use of functions,
taking such a type as argument.
File creation and opening functions will return /TREXIO file handles/,
namely pointers to ~trexio_s~ types. All functions accessing to the
TREXIO files will have as a first argument the TREXIO file handle.
#+begin_src c :tangle prefix_front.h
typedef struct trexio_s trexio_t;
#+end_src
#+begin_src c :tangle prefix_s_front.h
struct trexio_s {
char file_name[TREXIO_MAX_FILENAME_LENGTH];
pthread_mutex_t thread_lock;
back_end_t back_end;
char mode;
bool one_based;
int32_t state;
int16_t version_major;
int16_t version_minor;
int16_t version_patch;
char version[16];
};
#+end_src
File class for the Python API is defined below.
Use of Python class make it more intuitive and more python-ic
to work with TREXIO files.
#+begin_src python :tangle basic_python.py
class File:
"""trexio.File class.
General information about the TREXIO file.
Parameters:
filename: str
Is a name of the full path to the TREXIO file.
back_end: int
One of the currently supported TREXIO back ends.
For example, TREXIO_HDF5 (0) or TREXIO_TEXT (1).
mode: str
One of the currently supported TREXIO open modes.
For example, 'r' or 'w'.
state: int
Active state of the file (needed to write determinant_coefficient).
Default is 0.
isOpen: bool
Flag indicating whether the current object is still open for I/O
pytrexio_s:
A PyObject corresponding to SWIG proxy of the trexio_s struct in C.
This argument is in fact a TREXIO file handle, which is required for
communicating with the C back end.
info: dict
Dictionary of key-value pairs with additional information about the file.
"""
def __init__(self, filename, mode='r', back_end=TREXIO_HDF5,
pytrexio_s=None, info=None):
"""TREXIO File class constructor."""
self.filename = filename
self.mode = mode
self.state = 0
self.isOpen = False
self.exists = False
if pytrexio_s is None:
self.pytrexio_s = _open(filename, mode, back_end)
self.isOpen = True
self.exists = True
else:
self.pytrexio_s = pytrexio_s
self.isOpen = None
self.exists = None
self.back_end = self.pytrexio_s.back_end
self.info = info
def __enter__(self):
"""Enter statement for with ... as ... handling."""
return self
def __exit__(self, *args):
"""Exit statement for with ... as ... handling."""
if self.isOpen:
self.close()
def close(self):
"""Close a TREXIO File."""
if self.isOpen:
_close(self.pytrexio_s)
self.isOpen = False
else:
raise Exception("TREXIO File object has not been opened.")
def set_state(self, state):
"""Set the state of the TREXIO File."""
if not isinstance(state, int):
raise TypeError("state argument has to be int")
rc = pytr.trexio_set_state(self.pytrexio_s, state)
if rc != TREXIO_SUCCESS:
raise Error(rc)
self.state = state
def get_state(self):
"""Get the state of the TREXIO File."""
rc, state = pytr.trexio_get_state(self.pytrexio_s)
if rc != TREXIO_SUCCESS:
raise Error(rc)
if state != self.state:
raise Exception("Inconsistent state of the TREXIO file.")
return self.state
def inquire(self):
"""Inquire whether a TREXIO file exists."""
self.exists = _inquire(self.filename)
def __del__(self):
"""TREXIO File class destructor."""
if self.isOpen:
_close(self.pytrexio_s)
elif self.isOpen is None:
raise Exception("[WIP]: TREXIO file handle provided but what if the file is already closed?")
else:
pass
#+end_src
** File opening
~trexio_open~ creates a new TREXIO file or opens the existing one.
**Input parameters:**
1) ~file_name~ - string containing file name
2) ~mode~ - character containing open mode (see below)
- ~'w'~ - (write) creates a new file as READWRITE
- ~'r'~ - (read) opens existing file as READONLY
- ~'u'~ - (unsafe) opens existing file as READWRITE with the possibility to overwrite blocks and delete full groups.
3) ~back_end~ - integer number (or the corresponding global parameter) specifying the back end
- ~TREXIO_HDF5~ - for HDF5 back end (integer alternative: 0)
- ~TREXIO_TEXT~ - for TEXT back end (integer alternative: 1)
- ~TREXIO_AUTO~ - to automatically detect the applicable back end
**Output:**
- Pointer to the ~trexio_t~ (struct) file handle.
Upon creation of the TREXIO file, the ~package_version~ attribute of the
~metadata~ group is set to the ~TREXIO_PACKAGE_VERSION~ string.
This attribute **is not** automatically updated when the file is modified with
newer versions. However, this can be done manually by the user in unsafe mode.
**Note:** internal consistency is not guaranteed once the file has been modified in ~'u'~ (unsafe) mode.
Upon the first unsafe call to ~trexio_open~ the ~unsafe~ attribute of the ~metadata~ group will be set
to 1 (true) in order to indicate that the file might be inconsistent due to the use of ~'u'~ mode.
**Note:** the ~file_name~ in TEXT back end actually corresponds to the
name of the directory where ~.txt~ data files are stored. The
actual name of each ~.txt~ file corresponds to the group name
provided in ~trex.config~ (e.g. ~nucleus.txt~ for nuclei-related
data). These names are populated by the generator.py (i.e. they
are hard-coded), which is why the user should tend to avoid
renaming the ~.txt~ data files.
*** C
#+begin_src c :tangle prefix_front.h :exports none
trexio_t* trexio_open(const char* file_name, const char mode,
const back_end_t back_end, trexio_exit_code* const rc_open);
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_t*
trexio_open(const char* file_name, const char mode,
const back_end_t back_end, trexio_exit_code* const rc_open)
{
if (file_name == NULL || file_name[0] == '\0') {
if (rc_open != NULL) *rc_open = TREXIO_INVALID_ARG_1;
return NULL;
}
/* Check overflow in file_name */
/* Check that the mode is valid */
if (mode != 'r' && mode != 'w' && mode != 'u') {
if (rc_open != NULL) *rc_open = TREXIO_INVALID_ARG_2;
return NULL;
}
/* Check that the back end is valid in non-read mode */
if ((back_end < 0 || back_end >= TREXIO_INVALID_BACK_END) && mode != 'r') {
if (rc_open != NULL) *rc_open = TREXIO_INVALID_ARG_3;
return NULL;
}
/* Check that the back end is valid in read-only mode */
if ((back_end < 0 || back_end > TREXIO_INVALID_BACK_END) && mode == 'r') {
if (rc_open != NULL) *rc_open = TREXIO_INVALID_ARG_3;
return NULL;
}
back_end_t back_end_local = back_end;
/* Try to determine the applicable backend if the back_end argument is TREXIO_AUTO */
if (back_end == TREXIO_AUTO && mode == 'r') {
#ifdef HAVE_HDF5
/* Check if the TREXIO file exists and if it is a directory */
trexio_exit_code rc_text = trexio_text_inquire(file_name);
if (rc_text == TREXIO_SUCCESS) {
back_end_local = TREXIO_TEXT;
} else {
/* If not, check if it is an HDF5 file */
trexio_exit_code rc_hdf5 = trexio_hdf5_inquire(file_name);
if (rc_hdf5 == TREXIO_SUCCESS) {
back_end_local = TREXIO_HDF5;
} else {
/* File is neither a directory nor an HDF5 file -> return an error */
if (rc_open != NULL) *rc_open = TREXIO_FILE_ERROR;
return NULL;
}
}
#else
/* In the current implementation if HDF5 back end is not available - then there is only back end left */
back_end_local = TREXIO_TEXT;
#endif
}
trexio_t* result = NULL;
void* result_tmp = NULL;
/* Allocate data structures */
switch (back_end_local) {
case TREXIO_TEXT:
result_tmp = malloc(sizeof(trexio_text_t));
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
result_tmp = malloc(sizeof(trexio_hdf5_t));
break;
#else
if (rc_open != NULL) *rc_open = TREXIO_BACK_END_MISSING;
return NULL;
#endif
default:
if (rc_open != NULL) *rc_open = TREXIO_FILE_ERROR;
return NULL;
/*
case TREXIO_JSON:
result = (trexio_t*) malloc (sizeof(trexio_json_t));
break;
,*/
}
result = (trexio_t*) result_tmp;
assert (result != NULL); /* TODO: Error handling */
/* Data for the parent type */
strncpy(result->file_name, file_name, TREXIO_MAX_FILENAME_LENGTH);
if (result->file_name[TREXIO_MAX_FILENAME_LENGTH-1] != '\0') {
if (rc_open != NULL) *rc_open = TREXIO_INVALID_ARG_1;
free(result);
return NULL;
}
result->back_end = back_end_local;
result->mode = mode;
result->one_based = false; // Need to be flipped in Fortran interface
result->state = 0; // By default the file corresponds to a ground state
int irc = pthread_mutex_init ( &(result->thread_lock), NULL);
if (irc != 0) {
if (rc_open != NULL) *rc_open = TREXIO_FAILURE;
free(result);
return NULL;
}
// assert (irc == 0);
trexio_exit_code rc;
/* Back end initialization */
rc = TREXIO_OPEN_ERROR;
switch (back_end_local) {
case TREXIO_TEXT:
rc = trexio_text_init(result);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_init(result);
break;
#else
if (rc_open != NULL) *rc_open = TREXIO_BACK_END_MISSING;
free(result);
return NULL;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_init(result);
break;
,*/
}
if (rc != TREXIO_SUCCESS) {
if (rc_open != NULL) *rc_open = TREXIO_OPEN_ERROR;
free(result);
return NULL;
}
/* File locking */
rc = TREXIO_LOCK_ERROR;
switch (back_end_local) {
case TREXIO_TEXT:
rc = trexio_text_lock(result);
break;
/* HDF5 v.>=1.10 has file locking activated by default */
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = TREXIO_SUCCESS;
break;
#else
if (rc_open != NULL) *rc_open = TREXIO_BACK_END_MISSING;
free(result);
return NULL;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_lock(result);
break;
,*/
}
if (rc != TREXIO_SUCCESS) {
if (rc_open != NULL) *rc_open = TREXIO_LOCK_ERROR;
free(result);
return NULL;
}
/* Write metadata (i.e. package version) upon creation */
rc = trexio_has_metadata_package_version(result);
if (rc == TREXIO_FAILURE) {
if (rc_open != NULL) *rc_open = TREXIO_OPEN_ERROR;
free(result);
return NULL;
}
if (rc == TREXIO_HAS_NOT) {
/* Write TREXIO_PACKAGE_VERSION upon creation of the file */
switch (back_end_local) {
case TREXIO_TEXT:
rc = trexio_text_write_metadata_package_version(result, TREXIO_PACKAGE_VERSION);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_metadata_package_version(result, TREXIO_PACKAGE_VERSION);
break;
#else
if (rc_open != NULL) *rc_open = TREXIO_BACK_END_MISSING;
free(result);
return NULL;
#endif
}
if (rc != TREXIO_SUCCESS) {
if (rc_open != NULL) *rc_open = rc;
free(result);
return NULL;
}
result->version_major = TREXIO_VERSION_MAJOR;
result->version_minor = TREXIO_VERSION_MINOR;
result->version_patch = TREXIO_VERSION_PATCH;
strncpy(result->version, TREXIO_PACKAGE_VERSION, 16);
} else {
/* Otherwise read the metadata_package_version to get the TREXIO version upon creation of the file */
char version_origin[16];
switch (back_end_local) {
case TREXIO_TEXT:
rc = trexio_text_read_metadata_package_version(result, version_origin, 16);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_read_metadata_package_version(result, version_origin, 16);
break;
#else
if (rc_open != NULL) *rc_open = TREXIO_BACK_END_MISSING;
free(result);
return NULL;
#endif
}
if (rc != TREXIO_SUCCESS) {
if (rc_open != NULL) *rc_open = rc;
free(result);
return NULL;
}
int16_t version_major, version_minor, version_patch;
int rc_scan = sscanf(version_origin,
"%3" SCNd16 ".%5" SCNd16 ".%5" SCNd16,
&version_major, &version_minor, &version_patch);
if (rc_scan != 3) {
if (rc_open != NULL) *rc_open = TREXIO_VERSION_PARSING_ISSUE;
free(result);
return NULL;
}
result->version_major = version_major;
result->version_minor = version_minor;
result->version_patch = version_patch;
strncpy(result->version, version_origin, 16);
}
if (result->version[15] != '\0' || result->version_major == 0) {
if (rc_open != NULL) *rc_open = TREXIO_FAILURE;
free(result);
return NULL;
}
/* Mark the file as unsafe upon opening in UNSAFE 'u' mode */
if (mode == 'u') {
rc = trexio_has_metadata_unsafe(result);
if (rc == TREXIO_FAILURE) {
if (rc_open != NULL) *rc_open = TREXIO_OPEN_ERROR;
free(result);
return NULL;
}
if (rc == TREXIO_HAS_NOT) {
int64_t unsafe_val = 1;
switch (back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_metadata_unsafe(result, unsafe_val);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_metadata_unsafe(result, unsafe_val);
break;
#else
if (rc_open != NULL) *rc_open = TREXIO_BACK_END_MISSING;
free(result);
return NULL;
#endif
}
}
if (rc != TREXIO_SUCCESS) {
if (rc_open != NULL) *rc_open = rc;
free(result);
return NULL;
}
}
/* Exit upon success */
if (rc_open != NULL) *rc_open = TREXIO_SUCCESS;
return result;
}
#+end_src
*** Fortran
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_t) function trexio_open_c (filename, mode, back_end, rc_open) bind(C, name="trexio_open")
use, intrinsic :: iso_c_binding
import
character(kind=c_char), dimension(*) :: filename
character(kind=c_char), intent(in), value :: mode
integer(trexio_back_end_t), intent(in), value :: back_end
integer(trexio_exit_code), intent(out) :: rc_open
end function trexio_open_c
end interface
#+end_src
*** Python
#+begin_src python :tangle basic_python.py
def _open(file_name: str, mode: str, back_end: int):
"""Create TREXIO file or open existing one.
Parameters:
file_name: str
Name of the TREXIO file
mode: str
One of the currently supported ~open~ modes (e.g. 'w', 'r')
back_end: int
One of the currently supported TREXIO back ends (e.g. TREXIO_HDF5, TREXIO_TEXT)
Return:
SWIG object of type trexio_s.
Examples:
>>> from trexio import open as tr_open
>>> trex_file = tr_open("example.h5", "w", TREXIO_HDF5)
"""
# The new trexio_open function is capable of returning error code which SWIG can append to the output trexio_s file struct
# However, if trexio_s* == NULL, then SWIG returns only an error code rc_open instead of a list [trexio_s, rc_open]
# Thus, the following try/except sequence is needed
try:
return_obj = pytr.trexio_open(file_name, mode, back_end)
assert return_obj is not None
if isinstance(return_obj, int):
raise Error(return_obj)
else:
rc_open = return_obj[1]
# this is a sanity check in case the code evolves and SWIG issue is patched
if rc_open == TREXIO_SUCCESS:
trexio_file = return_obj[0]
assert trexio_file is not None
except AssertionError:
raise Exception(f"Could not open TREXIO file {file_name} using trexio_open function. The return value is None (NULL pointer).")
return trexio_file
#+end_src
*** Zero-based versus one-based arrays of indices
Because arrays are zero-based in Fortran, we need to set a flag to
know if we need to shift by 1 arrays of indices.
#+begin_src c :tangle prefix_front.h :exports none
trexio_exit_code trexio_set_one_based(trexio_t* file);
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code trexio_set_one_based(trexio_t* file)
{
if (file == NULL) return TREXIO_FILE_ERROR;
file->one_based = true;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_set_one_based(trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_set_one_based
end interface
#+end_src
** File closing
~trexio_close~ closes an existing ~trexio_t~ file.
input parameters:
~file~ -- TREXIO file handle.
output:
~trexio_exit_code~ exit code.
*** C
#+begin_src c :tangle prefix_front.h :exports none
trexio_exit_code trexio_close(trexio_t* file);
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_close (trexio_t* file)
{
if (file == NULL) return TREXIO_FILE_ERROR;
trexio_exit_code rc = TREXIO_FAILURE;
assert(file->back_end < TREXIO_INVALID_BACK_END);
/* Things to be done before closing the file in the back-end */
rc = trexio_pre_close(file);
if (rc != TREXIO_SUCCESS) return rc;
/* Terminate the back end */
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_deinit(file);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_deinit(file);
break;
#else
FREE(file);
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_deinit(file);
break;
,*/
}
if (rc != TREXIO_SUCCESS) {
FREE(file);
return rc;
}
/* File unlocking */
rc = TREXIO_UNLOCK_ERROR;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_unlock(file);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = TREXIO_SUCCESS;
break;
#else
FREE(file);
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_unlock(file);
break;
,*/
}
/* Terminate front end */
int irc = pthread_mutex_destroy( &(file->thread_lock) );
free(file);
if (irc != 0) return TREXIO_ERRNO;
if (rc != TREXIO_SUCCESS) return rc;
return TREXIO_SUCCESS;
}
#+end_src
*** Fortran
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_close (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_close
end interface
#+end_src
*** Python
#+begin_src python :tangle basic_python.py
def _close(trexio_file):
"""Close TREXIO file.
Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
"""
rc = pytr.trexio_close(trexio_file)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
** File existence
~trexio_inquire~ check whether TREXIO file exists.
input parameters:
~file_name~ - string containing file name
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).
*** C
#+begin_src c :tangle prefix_front.h :exports none
trexio_exit_code trexio_inquire(const char* file_name);
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_inquire (const char* file_name)
{
if (file_name == NULL || file_name[0] == '\0') return TREXIO_INVALID_ARG_1;
/* First check if the TREXIO file exists and if it is a directory */
trexio_exit_code rc_text = trexio_text_inquire(file_name);
#ifdef HAVE_HDF5
/* FILE_ERROR here means that the file exists but it is not a directory -> check with HDF5 */
if (rc_text == TREXIO_FILE_ERROR) {
trexio_exit_code rc_hdf5 = trexio_hdf5_inquire(file_name);
return rc_hdf5;
/* If rc_text is TREXIO_SUCCESS -> file is a TREXIO directory; TREXIO_FAILURE -> file/directory does not exist */
} else {
return rc_text;
}
#else
return rc_text;
#endif
}
#+end_src
*** Fortran
The function below is a C binding.
The front end Fortran function for ~trexio_inquire~ can be found in the ~Fortran helper/wrapper functions~.
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_inquire_c (filename) bind(C, name="trexio_inquire")
use, intrinsic :: iso_c_binding
import
character(kind=c_char), dimension(*) :: filename
end function trexio_inquire_c
end interface
#+end_src
*** Python
#+begin_src python :tangle basic_python.py
def _inquire(file_name: str) -> bool:
"""Check whether ~file_name~ TREXIO file exists.
"""
rc = pytr.trexio_inquire(trexio_file_name)
if rc == TREXIO_SUCCESS:
return True
elif rc == TREXIO_FAILURE:
return False
else:
raise Error(rc)
#+end_src
** File state
~trexio_set_state~ set an existing ~trexio_t~ file handle to a given state.
~trexio_get_state~ returns current sate of the ~trexio_t~ file handle.
input parameters:
~file~ -- TREXIO file handle.
~state~ -- ~int32_t~ number of state.
output:
~trexio_exit_code~ exit code.
*** C
#+begin_src c :tangle prefix_front.h :exports none
trexio_exit_code trexio_set_state(trexio_t* file, const int32_t num);
trexio_exit_code trexio_get_state(trexio_t* file, int32_t* const num);
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_set_state (trexio_t* file, const int32_t num)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
file->state = num;
return TREXIO_SUCCESS;
}
trexio_exit_code
trexio_get_state (trexio_t* file, int32_t* const num)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (num == NULL) return TREXIO_INVALID_ARG_2;
*num = file->state;
return TREXIO_SUCCESS;
}
#+end_src
*** Fortran
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_set_state (trex_file, state) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int32_t), intent(in), value :: state
end function trexio_set_state
end interface
interface
integer(trexio_exit_code) function trexio_get_state (trex_file, state) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int32_t), intent(out) :: state
end function trexio_get_state
end interface
#+end_src
*** Python
See TREXIO File Python class.
** Tasks to be done before closing
#+begin_src c :tangle trexio_private.h :exports none
trexio_exit_code trexio_pre_close(trexio_t* file);
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_pre_close (trexio_t* file)
{
if (file == NULL) return TREXIO_FILE_ERROR;
trexio_exit_code rc;
/* Check consistency between number of determinants and coefficients stored in the file */
if (file->version_major >= 2 && file->version_minor >= 2) {
bool has_det = (trexio_has_determinant_list(file) == TREXIO_SUCCESS);
bool has_coeff = (trexio_has_determinant_coefficient(file) == TREXIO_SUCCESS);
int64_t ndet, ncoeff;
if (has_det && has_coeff) {
rc = trexio_read_determinant_num_64(file, &ndet);
if (rc != TREXIO_SUCCESS) return rc;
rc = trexio_read_determinant_coefficient_size(file, &ncoeff);
if (rc != TREXIO_SUCCESS) return rc;
/* Maybe be even more direct and use assert here so that the user's code crushes in case of inconsistency */
if (ndet != ncoeff) return TREXIO_INVALID_DETERMINANT_NUM;
}
}
/* Up-spin and down-spin electrons */
int32_t nup, ndn, nelec;
bool has_up = (trexio_has_electron_up_num(file) == TREXIO_SUCCESS);
bool has_dn = (trexio_has_electron_dn_num(file) == TREXIO_SUCCESS);
bool has_updn = (trexio_has_electron_num(file) == TREXIO_SUCCESS);
if (file->mode != 'r') {
if (has_updn && has_up && has_dn) {
rc = trexio_read_electron_up_num(file, &nup);
if (rc != TREXIO_SUCCESS) return rc;
rc = trexio_read_electron_dn_num(file, &ndn);
if (rc != TREXIO_SUCCESS) return rc;
rc = trexio_read_electron_num(file, &nelec);
if (rc != TREXIO_SUCCESS) return rc;
if (nelec != nup + ndn) {
if (file->mode == 'u') {
nelec = nup + ndn;
rc = trexio_write_electron_num(file, nelec);
if (rc != TREXIO_SUCCESS) return rc;
} else {
return TREXIO_INVALID_ELECTRON_NUM;
}
}
} else if (has_up && has_dn) {
rc = trexio_read_electron_up_num(file, &nup);
if (rc != TREXIO_SUCCESS) return rc;
rc = trexio_read_electron_dn_num(file, &ndn);
if (rc != TREXIO_SUCCESS) return rc;
nelec = nup + ndn;
rc = trexio_write_electron_num(file, nelec);
if (rc != TREXIO_SUCCESS) return rc;
} else if (has_up) {
rc = trexio_read_electron_up_num(file, &nup);
if (rc != TREXIO_SUCCESS) return rc;
ndn = 0;
rc = trexio_write_electron_dn_num(file, ndn);
if (rc != TREXIO_SUCCESS) return rc;
nelec = nup;
rc = trexio_write_electron_num(file, nelec);
if (rc != TREXIO_SUCCESS) return rc;
} else if (has_dn) {
rc = trexio_read_electron_dn_num(file, &ndn);
if (rc != TREXIO_SUCCESS) return rc;
nup = 0;
rc = trexio_write_electron_up_num(file, nup);
if (rc != TREXIO_SUCCESS) return rc;
nelec = ndn;
rc = trexio_write_electron_num(file, nelec);
if (rc != TREXIO_SUCCESS) return rc;
}
}
return TREXIO_SUCCESS;
}
#+end_src
* Templates for front end
** Description
Consider the following block of =trex.json=:
#+begin_src python
{
"nucleus": {
"num" : [ "int" , [ ] ]
, "charge" : [ "float", [ "nucleus.num" ] ]
, "coord" : [ "float", [ "nucleus.num", "3" ] ]
, "label" : [ "str" , [ "nucleus.num" ] ]
, "point_group" : [ "str" , [ ] ]
}
}
#+end_src
~TREXIO~ is generated automatically by the ~generator.py~ Python
script based on the tree-like configuration provided in the
=trex.json= file. Because of that, generalized templates can be
implemented and re-used. This approach minimizes the number of bugs
as compared with manual copy-paste-modify scheme.
All templates presented below use the ~$var$~ notation to indicate
the variable, which will be replaced by the
~generator.py~. Sometimes the upper case is used, i.e. ~$VAR$~ (for
example, in ~#define~ statements). More detailed description of
each variable can be found below:
| Template variable | Description | Example |
|--------------------------------+-----------------------------------------------------+-------------------------------------|
| ~$group$~ | Name of the group | ~nucleus~ |
| ~$group_num$~ | Name of the numerical attribute (scalar) | ~nucleus_num~ |
| ~$group_str$~ | Name of the string attribute (scalar) | ~nucleus_point_group~ |
| ~$group_dset$~ | Name of the dataset (vector/matrix/tensor) | ~nucleus_coord~ |
| ~$group_dset_rank$~ | Rank of the dataset | ~2~ |
| ~$group_dset_dim$~ | Selected dimension of the dataset | ~nucleus_num~ |
| ~$group_dset_dim_list$~ | All dimensions of the dataset | ~{nucleus_num, 3}~ |
| ~$group_dset_dtype$~ | Basic type of the dataset (int/float/char) | ~float~ |
| ~$group_dset_h5_dtype$~ | Type of the dataset in HDF5 | ~double~ |
| ~$group_dset_format_scanf$~ | Input type of the dataset in TEXT [fscanf] | ~%lf~ |
| ~$group_dset_format_printf$~ | Output type of the dataset in TEXT [fprintf] | ~%24.16e~ |
| ~$group_dset_dtype_default$~ | Default datatype of the dataset [C] | ~double/int32_t~ |
| ~$group_dset_dtype_single$~ | Single precision datatype of the dataset [C] | ~float/int32_t~ |
| ~$group_dset_dtype_double$~ | Double precision datatype of the dataset [C] | ~double/int64_t~ |
| ~$group_dset_f_dtype_default$~ | Default datatype of the dataset [Fortran] | ~real(c_double)/integer(c_int32_t)~ |
| ~$group_dset_f_dtype_single$~ | Single precision datatype of the dataset [Fortran] | ~real(c_float)/integer(c_int32_t)~ |
| ~$group_dset_f_dtype_double$~ | Double precision datatype of the dataset [Fortran] | ~real(c_double)/integer(c_int64_t)~ |
| ~$group_dset_f_dims$~ | Dimensions in Fortran | ~(:,:)~ |
| ~$group_dset_py_dtype$~ | Standard datatype of the dataset [Python] | ~float/int~ |
| ~$default_prec$~ | Default precision for read/write without suffix [C] | ~64/32~ |
| ~$is_index$~ | Expands to ~true~ if dataset has a type ~index~ [C] | ~true/false~ |
Some of the aforementioned template variables with ~group_dset~ prefix are duplicated with ~group_num~ prefix,
e.g. you might find $group_num_dtype_double$ in the templates corresponding to numerical attributes.
The expanding values are the same as for ~group_dset~ and thus are not listed in the table above.
Note: parent group name is always added to the child objects upon
construction of TREXIO (e.g. ~num~ of ~nucleus~ group becomes
~nucleus_num~ and should be accessed accordingly within TREXIO).
TREXIO generator parses the =trex.json= file. TREXIO operates with
names of variables based on the 1-st (parent group) and 2-nd (child
object) levels of =trex.json= . The parsed data is divided in 2
parts:
1) Single attributes. These can be numerical values or strings.
2) Datasets. These can be vectors, matrices or tensors. The types are indicated in =trex.json=.
Currently supported data types: int, float and strings.
For each of the aforementioned objects, TREXIO provides *has*,
*read* and *write* functionality. TREXIO supports I/O with single
or double precision for integer and floating point numbers.
*Note:* single integer attributes that contain ~num~ in their name (e.g. ~nucleus_num~) are
considered dimensioning variables and cannot be negative or 0. An attempt to write negative or 0
value will result in ~TREXIO_INVALID_ARG_2~ exit code.
** Templates for front end has/read/write a single numerical attribute
*** Introduction
This section concerns API calls related to numerical attributes,
namely single value of int/float types.
| Function name | Description | Precision |
|-------------------------------+----------------------------------------+-----------|
| ~trexio_has_$group_num$~ | Check if an attribute exists in a file | --- |
| ~trexio_read_$group_num$~ | Read a attribute | Single |
| ~trexio_write_$group_num$~ | Write a attribute | Single |
| ~trexio_read_$group_num$_32~ | Read a attribute | Single |
| ~trexio_write_$group_num$_32~ | Write a attribute | Single |
| ~trexio_read_$group_num$_64~ | Read a attribute | Double |
| ~trexio_write_$group_num$_64~ | Write a attribute | Double |
*** C templates for front end
The ~C~ templates that correspond to each of the abovementioned
functions can be found below. First parameter is the ~TREXIO~ file
handle. Second parameter is the variable to be written/read
to/from the ~TREXIO~ file (except for ~trexio_has_~ functions).
Suffixes ~_32~ and ~_64~ correspond to API calls dealing with
single and real(c_double), respectively. The basic
(non-suffixed) API call on dimensioning variables deals with single
precision (see Table above).
**** Function declarations
#+begin_src c :tangle hrw_attr_num_front.h :exports none
trexio_exit_code trexio_has_$group_num$(trexio_t* const file);
trexio_exit_code trexio_read_$group_num$(trexio_t* const file, $group_num_dtype_default$* const num);
trexio_exit_code trexio_write_$group_num$(trexio_t* const file, const $group_num_dtype_default$ num);
trexio_exit_code trexio_read_$group_num$_32(trexio_t* const file, $group_num_dtype_single$* const num);
trexio_exit_code trexio_write_$group_num$_32(trexio_t* const file, const $group_num_dtype_single$ num);
trexio_exit_code trexio_read_$group_num$_64(trexio_t* const file, $group_num_dtype_double$* const num);
trexio_exit_code trexio_write_$group_num$_64(trexio_t* const file, const $group_num_dtype_double$ num);
#+end_src
**** Source code for double precision functions
#+begin_src c :tangle read_attr_num_64_front.c
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) {
case TREXIO_TEXT:
return trexio_text_read_$group_num$(file, num);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_read_$group_num$(file, num);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_read_$group_num$(file, num);
,*/
}
return TREXIO_FAILURE;
}
#+end_src
#+begin_src c :tangle write_attr_num_64_front.c
trexio_exit_code
trexio_write_$group_num$_64 (trexio_t* const file, const $group_num_dtype_double$ num)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
//if (num <= 0L) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_$group_num$(file, num);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_write_$group_num$(file, num);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_write_$group_num$(file, num);
,*/
}
return TREXIO_FAILURE;
}
#+end_src
**** Source code for single precision functions
#+begin_src c :tangle read_attr_num_32_front.c
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;
trexio_exit_code rc = TREXIO_GROUP_READ_ERROR;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_read_$group_num$(file, &num_64);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_read_$group_num$(file, &num_64);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break ;
#endif
/*
case TREXIO_JSON:
rc =trexio_json_read_$group_num$(file, &num_64);
break;
,*/
}
if (rc != TREXIO_SUCCESS) return rc;
,*num = ($group_num_dtype_single$) num_64;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle write_attr_num_32_front.c
trexio_exit_code
trexio_write_$group_num$_32 (trexio_t* const file, const $group_num_dtype_single$ num)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
//if (num <= 0) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num);
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
**** Source code for default functions
#+begin_src c :tangle read_attr_num_def_front.c
trexio_exit_code
trexio_read_$group_num$ (trexio_t* const file, $group_num_dtype_default$* const num)
{
return trexio_read_$group_num$_$default_prec$(file, num);
}
#+end_src
#+begin_src c :tangle write_attr_num_def_front.c
trexio_exit_code
trexio_write_$group_num$ (trexio_t* const file, const $group_num_dtype_default$ num)
{
return trexio_write_$group_num$_$default_prec$(file, num);
}
#+end_src
#+begin_src c :tangle has_attr_num_front.c
trexio_exit_code
trexio_has_$group_num$ (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_has_$group_num$(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_has_$group_num$(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_has_$group_num$(file);
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
*** Fortran templates for front end
The ~Fortran~ templates that provide an access to the ~C~ API calls from Fortran.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle write_attr_num_64_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_num$_64 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_double$, intent(in), value :: num
end function trexio_write_$group_num$_64
end interface
#+end_src
#+begin_src f90 :tangle read_attr_num_64_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_num$_64 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_double$, intent(out) :: num
end function trexio_read_$group_num$_64
end interface
#+end_src
#+begin_src f90 :tangle write_attr_num_32_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_num$_32 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_single$, intent(in), value :: num
end function trexio_write_$group_num$_32
end interface
#+end_src
#+begin_src f90 :tangle read_attr_num_32_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_num$_32 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_single$, intent(out) :: num
end function trexio_read_$group_num$_32
end interface
#+end_src
#+begin_src f90 :tangle write_attr_num_def_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_num$ (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_default$, intent(in), value :: num
end function trexio_write_$group_num$
end interface
#+end_src
#+begin_src f90 :tangle read_attr_num_def_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_num$ (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_default$, intent(out) :: num
end function trexio_read_$group_num$
end interface
#+end_src
#+begin_src f90 :tangle has_attr_num_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_has_$group_num$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_num$
end interface
#+end_src
*** Python templates for front end
#+begin_src python :tangle write_attr_num_front.py
def write_$group_num$(trexio_file, num_w: $group_num_py_dtype$) -> None:
"""Write the $group_num$ variable in the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
num_w: int
Value of the $group_num$ variable to be written.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_write_$group_num$(trexio_file.pytrexio_s, num_w)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
#+begin_src python :tangle read_attr_num_front.py
def read_$group_num$(trexio_file) -> $group_num_py_dtype$:
"""Read the $group_num$ variable from the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
~num_r~: int
Integer value of $group_num$ variable read from ~trexio_file~.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc, num_r = pytr.trexio_read_$group_num$(trexio_file.pytrexio_s)
if rc != TREXIO_SUCCESS:
raise Error(rc)
return num_r
#+end_src
#+begin_src python :tangle has_attr_num_front.py
def has_$group_num$(trexio_file) -> bool:
"""Check that $group_num$ variable exists in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
True if the variable exists, False otherwise
Raises:
- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_has_$group_num$(trexio_file.pytrexio_s)
if rc == TREXIO_FAILURE:
raise Error(rc)
return rc == TREXIO_SUCCESS
#+end_src
** Templates for front end has/read/write a dataset of numerical data
*** Introduction
This section concerns API calls related to datasets.
| Function name | Description | Precision |
|----------------------------------+--------------------------------------+-----------------------------|
| ~trexio_has_$group_dset$~ | Check if a dataset exists in a file | --- |
| ~trexio_read_$group_dset$~ | Read a dataset in default precision | Double/Single for float/int |
| ~trexio_write_$group_dset$~ | Write a dataset in default precision | Double/Single for float/int |
| ~trexio_read_safe_$group_dset$~ | Read a bounded dataset | Double |
| ~trexio_write_safe_$group_dset$~ | Write a bounded dataset | Double |
| ~trexio_read_$group_dset$_32~ | Read a dataset in single precision | Single |
| ~trexio_write_$group_dset$_32~ | Write a dataset in single precision | Single |
| ~trexio_read_$group_dset$_64~ | Read a dataset in double precision | Double |
| ~trexio_write_$group_dset$_64~ | Write a dataset in double precision | Double |
*** C templates for front end
The C templates that correspond to each of the abovementioned functions can be found below.
First parameter is the ~TREXIO~ file handle. Second parameter is the variable to be written/read
to/from the ~TREXIO~ file (except for ~trexio_has_~ functions).
Suffixes ~_32~ and ~_64~ correspond to API calls dealing with single and double precision, respectively.
The basic (non-suffixed) API call on datasets deals with real(c_double) (see Table above).
**** Function declarations
#+begin_src c :tangle hrw_dset_data_front.h :exports none
trexio_exit_code trexio_has_$group_dset$(trexio_t* const file);
trexio_exit_code trexio_read_$group_dset$(trexio_t* const file, $group_dset_dtype_default$* const $group_dset$);
trexio_exit_code trexio_write_$group_dset$(trexio_t* const file, const $group_dset_dtype_default$* $group_dset$);
trexio_exit_code trexio_read_$group_dset$_32(trexio_t* const file, $group_dset_dtype_single$* const $group_dset$);
trexio_exit_code trexio_write_$group_dset$_32(trexio_t* const file, const $group_dset_dtype_single$* $group_dset$);
trexio_exit_code trexio_read_$group_dset$_64(trexio_t* const file, $group_dset_dtype_double$* const $group_dset$);
trexio_exit_code trexio_write_$group_dset$_64(trexio_t* const file, const $group_dset_dtype_double$* $group_dset$);
trexio_exit_code trexio_read_safe_$group_dset$(trexio_t* const file, $group_dset_dtype_default$* const dset_out, const int64_t dim_out);
trexio_exit_code trexio_write_safe_$group_dset$(trexio_t* const file, const $group_dset_dtype_default$* dset_in, const int64_t dim_in);
trexio_exit_code trexio_read_safe_$group_dset$_32(trexio_t* const file, $group_dset_dtype_single$* const dset_out, const int64_t dim_out);
trexio_exit_code trexio_write_safe_$group_dset$_32(trexio_t* const file, const $group_dset_dtype_single$* dset_in, const int64_t dim_in);
trexio_exit_code trexio_read_safe_$group_dset$_64(trexio_t* const file, $group_dset_dtype_double$* const dset_out, const int64_t dim_out);
trexio_exit_code trexio_write_safe_$group_dset$_64(trexio_t* const file, const $group_dset_dtype_double$* dset_in, const int64_t dim_in);
#+end_src
**** Source code for double precision functions
#+begin_src c :tangle read_dset_data_64_front.c
trexio_exit_code
trexio_read_$group_dset$_64 (trexio_t* const file, $group_dset_dtype_double$* const $group_dset$)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
uint32_t rank = $group_dset_rank$;
uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
assert(file->back_end < TREXIO_INVALID_BACK_END);
rc = TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_read_$group_dset$(file, $group_dset$, rank, dims);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_read_$group_dset$(file, $group_dset$, rank, dims);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_read_$group_dset$(file, $group_dset$, rank, dims);
break;
,*/
}
if (rc != TREXIO_SUCCESS) return rc;
/* Handle index type */
if ($is_index$) {
uint64_t dim_size = 1;
for (uint32_t i=0; i<rank; ++i){
dim_size *= dims[i];
}
for (uint64_t i=0; i<dim_size; ++i){
$group_dset$[i] += ($group_dset_dtype_double$) 1;
}
}
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle write_dset_data_64_front.c
trexio_exit_code
trexio_write_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_double$* $group_dset$)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
uint32_t rank = $group_dset_rank$;
uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
if ($is_index$) {
/* Handle index type : is_index = $is_index$ */
uint64_t dim_size = 1;
for (uint32_t i=0; i<rank; ++i){
dim_size *= dims[i];
}
$group_dset_dtype_double$* $group_dset$_p =
CALLOC(dim_size, $group_dset_dtype_double$);
if ($group_dset$_p == NULL) return TREXIO_ALLOCATION_FAILED;
for (uint64_t i=0; i<dim_size; ++i){
$group_dset$_p[i] = $group_dset$[i] - ($group_dset_dtype_double$) 1;
}
rc = TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_$group_dset$(file,
(const $group_dset_dtype_double$*) $group_dset$_p,
rank, dims);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_$group_dset$(file,
(const $group_dset_dtype_double$*) $group_dset$_p,
rank, dims);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_write_$group_dset$(file, $group_dset$_p, rank, dims);
break;
,*/
FREE($group_dset$_p);
}
} else {
rc = TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_$group_dset$(file, $group_dset$, rank, dims);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_$group_dset$(file, $group_dset$, rank, dims);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_write_$group_dset$(file, $group_dset$, rank, dims);
break;
,*/
}
}
return rc;
}
#+end_src
**** Source code for single precision functions
#+begin_src c :tangle read_dset_data_32_front.c
trexio_exit_code
trexio_read_$group_dset$_32 (trexio_t* const file, $group_dset_dtype_single$* const $group_dset$)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
uint32_t rank = $group_dset_rank$;
uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
uint64_t dim_size = 1;
for (uint32_t i=0; i<rank; ++i){
dim_size *= dims[i];
}
$group_dset_dtype_double$* $group_dset$_64 = CALLOC(dim_size, $group_dset_dtype_double$);
if ($group_dset$_64 == NULL) return TREXIO_ALLOCATION_FAILED;
assert(file->back_end < TREXIO_INVALID_BACK_END);
rc = TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_read_$group_dset$(file, $group_dset$_64, rank, dims);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_read_$group_dset$(file, $group_dset$_64, rank, dims);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_read_$group_dset$(file, $group_dset$_64, rank, dims);
break;
,*/
}
if (rc != TREXIO_SUCCESS){
FREE($group_dset$_64);
return rc;
}
if ($is_index$) {
for (uint64_t i=0; i<dim_size; ++i){
$group_dset$[i] = ($group_dset_dtype_single$) $group_dset$_64[i] + 1;
}
} else {
for (uint64_t i=0; i<dim_size; ++i){
$group_dset$[i] = ($group_dset_dtype_single$) $group_dset$_64[i];
}
}
FREE($group_dset$_64);
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle write_dset_data_32_front.c
trexio_exit_code
trexio_write_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_single$* $group_dset$)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
uint32_t rank = $group_dset_rank$;
uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
uint64_t dim_size = 1;
for (uint32_t i=0; i<rank; ++i){
dim_size *= dims[i];
}
$group_dset_dtype_double$* $group_dset$_64 = CALLOC(dim_size, $group_dset_dtype_double$);
if ($group_dset$_64 == NULL) return TREXIO_ALLOCATION_FAILED;
/* A type conversion from single precision to double required since back end only accepts 64-bit data */
if ($is_index$) {
for (uint64_t i=0; i<dim_size; ++i){
$group_dset$_64[i] = ($group_dset_dtype_double$) $group_dset$[i] - ($group_dset_dtype_double$) 1;
}
} else {
for (uint64_t i=0; i<dim_size; ++i){
$group_dset$_64[i] = ($group_dset_dtype_double$) $group_dset$[i];
}
}
assert(file->back_end < TREXIO_INVALID_BACK_END);
rc = TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_$group_dset$(file, $group_dset$_64, rank, dims);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_$group_dset$(file, $group_dset$_64, rank, dims);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_write_$group_dset$(file, $group_dset$_64, rank, dims);
break;
,*/
}
FREE($group_dset$_64);
if (rc != TREXIO_SUCCESS) return rc;
return TREXIO_SUCCESS;
}
#+end_src
**** Source code for memory-safe functions
#+NAME:dimCheck
#+begin_src c
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
uint32_t rank = $group_dset_rank$;
uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
/* The block below is specific to safe API as it checks the boundaries */
uint64_t dim_size = 1;
for (uint32_t i=0; i<rank; ++i){
dim_size *= dims[i];
}
#+end_src
#+begin_src c :tangle read_dset_data_32_safe_front.c :noweb yes
trexio_exit_code
trexio_read_safe_$group_dset$_32 (trexio_t* const file, $group_dset_dtype_single$* const dset_out, const int64_t dim_out)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_out == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
<<dimCheck>>
if (dim_out > (int64_t) dim_size) return TREXIO_UNSAFE_ARRAY_DIM;
return trexio_read_$group_dset$_32(file, dset_out);
}
#+end_src
#+begin_src c :tangle write_dset_data_32_safe_front.c :noweb yes
trexio_exit_code
trexio_write_safe_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_single$* dset_in, const int64_t dim_in)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
<<dimCheck>>
if (dim_in > (int64_t) dim_size) return TREXIO_UNSAFE_ARRAY_DIM;
return trexio_write_$group_dset$_32(file, dset_in);
}
#+end_src
#+begin_src c :tangle read_dset_data_64_safe_front.c :noweb yes
trexio_exit_code
trexio_read_safe_$group_dset$_64 (trexio_t* const file, $group_dset_dtype_double$* const dset_out, const int64_t dim_out)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_out == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
<<dimCheck>>
if (dim_out > (int64_t) dim_size) return TREXIO_UNSAFE_ARRAY_DIM;
return trexio_read_$group_dset$_64(file, dset_out);
}
#+end_src
#+begin_src c :tangle write_dset_data_64_safe_front.c :noweb yes
trexio_exit_code
trexio_write_safe_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_double$* dset_in, const int64_t dim_in)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
<<dimCheck>>
if (dim_in > (int64_t) dim_size) return TREXIO_UNSAFE_ARRAY_DIM;
return trexio_write_$group_dset$_64(file, dset_in);
}
#+end_src
**** Source code for default functions
#+begin_src c :tangle read_dset_data_safe_def_front.c
trexio_exit_code
trexio_read_safe_$group_dset$ (trexio_t* const file, $group_dset_dtype_default$* const $group_dset$, const int64_t dim_out)
{
return trexio_read_safe_$group_dset$_$default_prec$(file, $group_dset$, dim_out);
}
#+end_src
#+begin_src c :tangle write_dset_data_safe_def_front.c
trexio_exit_code
trexio_write_safe_$group_dset$ (trexio_t* const file, const $group_dset_dtype_default$* $group_dset$, const int64_t dim_in)
{
return trexio_write_safe_$group_dset$_$default_prec$(file, $group_dset$, dim_in);
}
#+end_src
#+begin_src c :tangle read_dset_data_def_front.c
trexio_exit_code
trexio_read_$group_dset$ (trexio_t* const file, $group_dset_dtype_default$* const $group_dset$)
{
return trexio_read_$group_dset$_$default_prec$(file, $group_dset$);
}
#+end_src
#+begin_src c :tangle write_dset_data_def_front.c
trexio_exit_code
trexio_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype_default$* $group_dset$)
{
return trexio_write_$group_dset$_$default_prec$(file, $group_dset$);
}
#+end_src
#+begin_src c :tangle has_dset_data_front.c
trexio_exit_code
trexio_has_$group_dset$ (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_has_$group_dset$(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_has_$group_dset$(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_has_$group_dset$(file);
,*/
}
return TREXIO_FAILURE;
}
#+end_src
*** Fortran templates for front end
The ~Fortran~ templates that provide an access to the ~C~ API calls from ~Fortran~.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle write_dset_data_64_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_dset$_64 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_double$, intent(in) :: dset$group_dset_f_dims$
end function trexio_write_$group_dset$_64
end interface
#+end_src
#+begin_src f90 :tangle read_dset_data_64_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_dset$_64 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_double$, intent(out) :: dset$group_dset_f_dims$
end function trexio_read_$group_dset$_64
end interface
#+end_src
#+begin_src f90 :tangle write_dset_data_32_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_dset$_32 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_single$, intent(in) :: dset$group_dset_f_dims$
end function trexio_write_$group_dset$_32
end interface
#+end_src
#+begin_src f90 :tangle read_dset_data_32_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_dset$_32 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_single$, intent(out) :: dset$group_dset_f_dims$
end function trexio_read_$group_dset$_32
end interface
#+end_src
#+begin_src f90 :tangle write_dset_data_def_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_dset$ (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_default$, intent(in) :: dset$group_dset_f_dims$
end function trexio_write_$group_dset$
end interface
#+end_src
#+begin_src f90 :tangle read_dset_data_def_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_dset$ (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_default$, intent(out) :: dset$group_dset_f_dims$
end function trexio_read_$group_dset$
end interface
#+end_src
#+begin_src f90 :tangle has_dset_data_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_has_$group_dset$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_dset$
end interface
#+end_src
*** Python templates for front end
#+begin_src python :tangle write_dset_data_front.py
def write_$group_dset$(trexio_file, dset_w) -> None:
"""Write the $group_dset$ array of numbers in the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
dset_w: list OR numpy.ndarray
Array of $group_dset$ values to be written. If array data type does not correspond to int64 or float64, the conversion is performed.
Raises:
- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
doConversion = False
doFlatten = False
if not isinstance(dset_w, (list, tuple)):
# if input array is not a list or tuple then it is probably a numpy array
if isinstance(dset_w, np.ndarray) and (not dset_w.dtype==np.int64 or not dset_w.dtype==np.float64):
doConversion = True
if len(dset_w.shape) > 1:
doFlatten = True
if doConversion:
dset_64 = np.$group_dset_py_dtype$64(dset_w).flatten()
else:
dset_flat = np.array(dset_w, dtype=np.$group_dset_py_dtype$64).flatten()
else:
if doConversion:
dset_64 = np.$group_dset_py_dtype$64(dset_w)
else:
# if input array is a multidimensional list or tuple, we have to convert it
try:
doFlatten = True
ncol = len(dset_w[0])
dset_flat = np.array(dset_w, dtype=np.$group_dset_py_dtype$64).flatten()
except TypeError:
doFlatten = False
pass
if doConversion:
rc = pytr.trexio_write_safe_$group_dset$_64(trexio_file.pytrexio_s, dset_64)
elif doFlatten:
rc = pytr.trexio_write_safe_$group_dset$_64(trexio_file.pytrexio_s, dset_flat)
else:
rc = pytr.trexio_write_safe_$group_dset$_64(trexio_file.pytrexio_s, dset_w)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
#+begin_src python :tangle read_dset_data_front.py
def read_$group_dset$(trexio_file, dim = None, doReshape = None, dtype = None):
"""Read the $group_dset$ array of numbers from the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
dim (Optional): int
Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
If None, the function will read all necessary array dimensions from the file.
dtype (Optional): type
NumPy data type of the output (e.g. np.int32|int16 or np.float32|float16). If specified, the output array will be converted from the default double precision.
doReshape (Optional): bool
Flag to determine whether the output NumPy array has be reshaped or not. Be default, reshaping is performed
based on the dimensions from the ~trex.json~ file. Otherwise, ~shape~ array (list or tuple) is used if provided by the user.
Returns:
~dset_64~ if dtype is None or ~dset_converted~ otherwise: numpy.ndarray
1D NumPy array with ~dim~ elements corresponding to $group_dset$ values read from the TREXIO file.
Raises:
- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
if doReshape is None:
doReshape = True
# if dim is not specified, read dimensions from the TREXIO file
dims_list = None
if dim is None or doReshape:
$group_dset_dim$ = read_$group_dset_dim$(trexio_file)
dims_list = [$group_dset_dim_list$]
dim = 1
for i in range($group_dset_rank$):
dim *= dims_list[i]
shape = tuple(dims_list)
if shape is None and doReshape:
raise ValueError("Reshaping failure: shape is None.")
rc, dset_64 = pytr.trexio_read_safe_$group_dset$_64(trexio_file.pytrexio_s, dim)
if rc != TREXIO_SUCCESS:
raise Error(rc)
isConverted = False
dset_converted = None
if dtype is not None:
try:
assert isinstance(dtype, type)
except AssertionError:
raise TypeError("dtype argument has to be an instance of the type class (e.g. np.float32).")
if not dtype==np.int64 or not dtype==np.float64:
dset_converted = np.array(dset_64, dtype=dtype)
isConverted = True
# additional assert can be added here to check that read_safe functions returns numpy array of proper dimension
if doReshape:
# in-place reshaping did not work so I have to make a copy
if isConverted:
dset_reshaped = np.reshape(dset_converted, shape, order='C')
else:
dset_reshaped = np.reshape(dset_64, shape, order='C')
if isConverted:
return dset_converted
elif doReshape:
return dset_reshaped
else:
return dset_64
#+end_src
#+begin_src python :tangle has_dset_data_front.py
def has_$group_dset$(trexio_file) -> bool:
"""Check that $group_dset$ variable exists in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
True if the variable exists, False otherwise
Raises:
- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_has_$group_dset$(trexio_file.pytrexio_s)
if rc == TREXIO_FAILURE:
raise Error(rc)
return rc == TREXIO_SUCCESS
#+end_src
** Templates for front end has/read/write a dataset of sparse data
*** Introduction
Sparse data structures are used typically for large tensors such as
two-electron integrals. For example, in the =trex.json= file sparse
arrays appear as for the ~eri~ :
#+begin_src python
"ao_2e_int" : {
"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
}
#+end_src
The electron repulsion integral (eri) $\langle ij | kl \rangle$ is
represented as a quartet of integers $(i,j,k,l)$ and a floating
point value.
To store $N$ integrals in the file, we store
- An array of quartets of integers
- An array of values (floats)
Both arrays have the same size, $N$, the number of non-zero integrals.
Knowing the maximum dimensions allows to check that the integers are
in a valid range, and also lets the library choose the smallest
integer representation to compress the storage.
Fortran uses 1-based array indexing, while C uses 0-based indexing.
Internally, we use a 0-based representation but the Fortran binding
does the appropriate conversion when reading or writing.
As the number of integrals to store can be prohibitively large, we
provide the possibility to read/write the integrals in chunks. So the
functions take two extra parameters:
- ~offset_file~ : how many integrals in the file should be skipped when reading/writing.
An offset of zero implies to read the first integral.
- ~buffer_size~ : the number of integrals to read/write.
If EOF is encountered upon reading, the ~buffer_size~ is overwritten with the number
of integrals that have been read before EOF and the ~trexio_read_~ function return
~TREXIO_END~ exit code instead of ~TREXIO_SUCCESS~.
The storage of ~int~ indices is internally compressed based on the maximum possible value of an index,
which is derived from the corresponding dimension of the sparse array (e.g. ~ao_num~ is the upper bound
of indices in the aforementioned ~ao_2e_int_eri~ dataset).
The upper bounds for different ~int~ types (e.g. ~uint16_t~) can be found in the in the =stdint.h= C library.
Currently implemented list of compressions based on the upper bound of indices can be found below:
| Max value of indices | Internal representation (in the TREXIO file) |
|---------------------------------+----------------------------------------------|
| ~UINT8_MAX~ (e.g. $< 255$) | 8-bit unsigned int |
| ~UINT16_MAX~ (e.g. $< 65535$) | 16-bit unsigned int |
| Otherwise (e.g. $\ge 65535$) | 32-bit signed int |
This section concerns API calls related to sparse data structures.
| Function name | Description | Precision |
|----------------------------------+-------------------------------------------------------------+----------------------------------|
| ~trexio_has_$group_dset$~ | Check if a sparse dset is present in a file | --- |
| ~trexio_read_$group_dset$~ | Read indices and values of a sparse dset | Single/Double for indices/values |
| ~trexio_read_$group_dset$_size~ | Read the number of sparse data elements stored in the file | Double for size |
| ~trexio_write_$group_dset$~ | Write indices and values of a sparse dset | Single/Double for indices/values |
| ~trexio_read_safe_$group_dset$~ | Safe (bounded) read of indices and values (for Python API) | Single/Double for indices/values |
| ~trexio_write_safe_$group_dset$~ | Safe (bounded) write of indices and values (for Python API) | Single/Double for indices/values |
*** C templates for front end
**** Function declarations
#+begin_src c :tangle hrw_dset_sparse_front.h :exports none
trexio_exit_code trexio_has_$group_dset$(trexio_t* const file);
trexio_exit_code trexio_read_$group_dset$(trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size, int32_t* const index_sparse, double* const value_sparse);
trexio_exit_code trexio_read_$group_dset$_size(trexio_t* const file, int64_t* const size_max);
trexio_exit_code trexio_write_$group_dset$(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int32_t* index_sparse, const double* value_sparse);
trexio_exit_code trexio_read_safe_$group_dset$(trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size_read, int32_t* const index_sparse_read, const int64_t size_index_read, double* const value_sparse_read, const int64_t size_value_read);
trexio_exit_code trexio_write_safe_$group_dset$(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int32_t* index_sparse_write, const int64_t size_index_write, const double* value_sparse_write, const int64_t size_value_write);
#+end_src
**** Source code for default functions
#+begin_src c :tangle read_dset_sparse_front.c
trexio_exit_code trexio_read_safe_$group_dset$(trexio_t* const file,
const int64_t offset_file,
int64_t* const buffer_size_read,
int32_t* const index_sparse_read,
const int64_t size_index_read,
double* const value_sparse_read,
const int64_t size_value_read
)
{
return trexio_read_$group_dset$(file, offset_file, buffer_size_read, index_sparse_read, value_sparse_read);
}
trexio_exit_code
trexio_read_$group_dset$(trexio_t* const file,
const int64_t offset_file,
int64_t* const buffer_size,
int32_t* const index_sparse,
double* const value_sparse
)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (offset_file < 0L) return TREXIO_INVALID_ARG_2;
if (*buffer_size <= 0L) return TREXIO_INVALID_ARG_3;
if (index_sparse == NULL) return TREXIO_INVALID_ARG_4;
if (value_sparse == NULL) return TREXIO_INVALID_ARG_5;
if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
const uint32_t rank = $group_dset_rank$; // To be set by generator : number of indices
int64_t size_max; // Max number of integrals (already in the file)
trexio_exit_code rc;
/* Read the max number of integrals stored in the file */
rc = trexio_read_$group_dset$_size(file, &size_max);
if (rc != TREXIO_SUCCESS) return rc;
int64_t num;
rc = trexio_read_$group_dset_sparse_dim$_64(file, &num);
if (rc != TREXIO_SUCCESS) return rc;
// introduce a new variable which will be modified with the number of integrals being read if EOF is encountered
int64_t eof_read_size = 0L;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_read_$group_dset$(file, offset_file, *buffer_size, num, &eof_read_size, index_sparse, value_sparse);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_read_$group_dset$(file, offset_file, *buffer_size, num, &eof_read_size, index_sparse, value_sparse);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
return trexio_json_read_$group_dset$(...);
break;
,*/
default:
rc = TREXIO_FAILURE; /* Impossible case */
break;
}
if (rc != TREXIO_SUCCESS && rc != TREXIO_END) return rc;
if (rc == TREXIO_END) *buffer_size = eof_read_size;
// shift indices to be one-based if Fortran API is used
if (file->one_based) {
// if EOF is reached - shift only indices that have been read, not an entire buffer
uint64_t index_size = rank*(*buffer_size) ;
for (uint64_t i=0; i<index_size; ++i){
index_sparse[i] += 1;
}
}
return rc;
}
#+end_src
#+begin_src c :tangle read_dset_sparse_size_front.c
trexio_exit_code
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) {
case TREXIO_TEXT:
return trexio_text_read_$group_dset$_size(file, size_max);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_read_$group_dset$_size(file, size_max);
break;
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_read_$group_dset$_size(...);
break;
,*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}
#+end_src
#+begin_src c :tangle write_dset_sparse_front.c
trexio_exit_code trexio_write_safe_$group_dset$(trexio_t* const file,
const int64_t offset_file,
const int64_t buffer_size,
const int32_t* index_sparse_write,
const int64_t size_index_write,
const double* value_sparse_write,
const int64_t size_value_write
)
{
return trexio_write_$group_dset$(file, offset_file, buffer_size, index_sparse_write, value_sparse_write);
}
trexio_exit_code
trexio_write_$group_dset$(trexio_t* const file,
const int64_t offset_file,
const int64_t buffer_size,
const int32_t* index_sparse,
const double* value_sparse
)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (offset_file < 0L) return TREXIO_INVALID_ARG_2;
if (buffer_size <= 0L) return TREXIO_INVALID_ARG_3;
if (index_sparse == NULL) return TREXIO_INVALID_ARG_4;
if (value_sparse == NULL) return TREXIO_INVALID_ARG_5;
const uint32_t rank = $group_dset_rank$; // To be set by generator : number of indices
int64_t size_max=0L; // Max number of integrals (already in the file)
trexio_exit_code rc;
/* Read the max number of integrals stored in the file */
rc = trexio_read_$group_dset$_size(file, &size_max);
if (rc != TREXIO_SUCCESS && rc != TREXIO_DSET_MISSING) return rc;
if (rc == TREXIO_DSET_MISSING) size_max = 0L;
int64_t num;
rc = trexio_read_$group_dset_sparse_dim$_64(file, &num);
if (rc != TREXIO_SUCCESS) return rc;
// shift indices to be zero-based if Fortran API is used
if (file->one_based) {
uint64_t index_size = rank * buffer_size;
int32_t* index_sparse_p = CALLOC(index_size, int32_t);
if (index_sparse_p == NULL) return TREXIO_ALLOCATION_FAILED;
for (uint64_t i=0; i<index_size; ++i){
index_sparse_p[i] = index_sparse[i] - 1;
}
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_$group_dset$(file, offset_file, buffer_size, num,
size_max, index_sparse_p, value_sparse);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_$group_dset$(file, offset_file, buffer_size, num,
index_sparse_p, value_sparse);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_write_$group_dset$(...);
break;
,*/
default:
rc = TREXIO_FAILURE; /* Impossible case */
break;
}
FREE(index_sparse_p);
}
else {
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_$group_dset$(file, offset_file, buffer_size, num,
size_max, index_sparse, value_sparse);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_$group_dset$(file, offset_file, buffer_size, num,
index_sparse, value_sparse);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_write_$group_dset$(...);
break;
,*/
default:
rc = TREXIO_FAILURE; /* Impossible case */
break;
}
}
return rc;
}
#+end_src
#+begin_src c :tangle has_dset_sparse_front.c
trexio_exit_code
trexio_has_$group_dset$ (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_has_$group_dset$(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_has_$group_dset$(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_has_$group_dset$(file);
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
*** Fortran templates for front end
The ~Fortran~ templates that provide an access to the ~C~ API calls from ~Fortran~.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle write_dset_sparse_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_dset$ (trex_file, &
offset_file, buffer_size, &
index_sparse, value_sparse) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size
integer(c_int32_t), intent(in) :: index_sparse(*)
real(c_double), intent(in) :: value_sparse(*)
end function trexio_write_$group_dset$
end interface
interface
integer(trexio_exit_code) function trexio_write_safe_$group_dset$ (trex_file, &
offset_file, buffer_size, &
index_sparse, index_size, &
value_sparse, value_size) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size
integer(c_int32_t), intent(in) :: index_sparse(*)
integer(c_int64_t), intent(in), value :: index_size
real(c_double), intent(in) :: value_sparse(*)
integer(c_int64_t), intent(in), value :: value_size
end function trexio_write_safe_$group_dset$
end interface
#+end_src
#+begin_src f90 :tangle read_dset_sparse_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_dset$ (trex_file, &
offset_file, buffer_size, &
index_sparse, value_sparse) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size
integer(c_int32_t), intent(out) :: index_sparse(*)
real(c_double), intent(out) :: value_sparse(*)
end function trexio_read_$group_dset$
end interface
interface
integer(trexio_exit_code) function trexio_read_safe_$group_dset$ (trex_file, &
offset_file, buffer_size, &
index_sparse, index_size, &
value_sparse, value_size) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size
integer(c_int32_t), intent(out) :: index_sparse(*)
integer(c_int64_t), intent(in), value :: index_size
real(c_double), intent(out) :: value_sparse(*)
integer(c_int64_t), intent(in), value :: value_size
end function trexio_read_safe_$group_dset$
end interface
#+end_src
#+begin_src f90 :tangle read_dset_sparse_size_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_dset$_size (trex_file, &
size_max) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(out) :: size_max
end function trexio_read_$group_dset$_size
end interface
#+end_src
#+begin_src f90 :tangle has_dset_sparse_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_has_$group_dset$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_dset$
end interface
#+end_src
*** Python templates for front end
#+begin_src python :tangle write_dset_sparse_front.py
def write_$group_dset$(trexio_file: File, offset_file: int, buffer_size: int, indices: list, values: list) -> None:
"""Write the $group_dset$ indices and values in the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
offset_file: int
The number of integrals to be skipped in the file when writing.
buffer_size: int
The number of integrals to write in the file from the provided sparse arrays.
indices: list OR numpy.ndarray
Array of $group_dset$ indices to be written. If array data type does not correspond to int32, the conversion is performed.
values: list OR numpy.ndarray
Array of $group_dset$ values to be written. If array data type does not correspond to float64, the conversion is performed.
Raises:
- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
if not isinstance(offset_file, int):
raise TypeError("offset_file argument has to be an integer.")
if not isinstance(buffer_size, int):
raise TypeError("buffer_size argument has to be an integer.")
if not isinstance(indices, (list, tuple, np.ndarray)):
raise TypeError("indices argument has to be an array (list, tuple or NumPy ndarray).")
if not isinstance(values, (list, tuple, np.ndarray)):
raise TypeError("values argument has to be an array (list, tuple or NumPy ndarray).")
convertIndices = False
convertValues = False
flattenIndices = False
if isinstance(indices, np.ndarray):
# convert to int32 if input indices are in a different precision
if not indices.dtype==np.int32:
convertIndices = True
if len(indices.shape) > 1:
flattenIndices = True
if convertIndices:
indices_32 = np.int32(indices).flatten()
else:
indices_32 = np.array(indices, dtype=np.int32).flatten()
else:
if convertIndices:
indices_32 = np.int32(indices)
else:
# if input array is a multidimensional list or tuple, we have to convert it
try:
doFlatten = True
# if list of indices is flat - the attempt to compute len(indices[0]) will raise a TypeError
ncol = len(indices[0])
indices_32 = np.array(indices, dtype=np.int32).flatten()
except TypeError:
doFlatten = False
pass
if isinstance(values, np.ndarray):
# convert to float64 if input values are in a different precision
if not values.dtype==np.float64:
convertValues = True
if convertValues:
values_64 = np.float64(values)
if (convertIndices or flattenIndices) and convertValues:
rc = pytr.trexio_write_safe_$group_dset$(trexio_file.pytrexio_s, offset_file, buffer_size, indices_32, values_64)
elif (convertIndices or flattenIndices) and not convertValues:
rc = pytr.trexio_write_safe_$group_dset$(trexio_file.pytrexio_s, offset_file, buffer_size, indices_32, values)
elif not (convertIndices or flattenIndices) and convertValues:
rc = pytr.trexio_write_safe_$group_dset$(trexio_file.pytrexio_s, offset_file, buffer_size, indices, values_64)
else:
rc = pytr.trexio_write_safe_$group_dset$(trexio_file.pytrexio_s, offset_file, buffer_size, indices, values)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
#+begin_src python :tangle read_dset_sparse_front.py
def read_$group_dset$(trexio_file: File, offset_file: int, buffer_size: int) -> tuple:
"""Read the $group_dset$ indices and values from the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
offset_file: int
The number of integrals to be skipped in the file when reading.
buffer_size: int
The number of integrals to read from the file.
Returns:
(indices, values, n_int_read, eof_flag) tuple where
- indices and values are NumPy arrays [numpy.ndarray] with the default int32 and float64 precision, respectively;
- n_int_read [int] is the number of integrals read from the trexio_file
(either strictly equal to buffer_size or less than buffer_size if EOF has been reached);
- eof_flag [bool] is True when EOF has been reached (i.e. when call to low-level pytrexio API returns TREXIO_END)
False otherwise.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS
and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
if not isinstance(offset_file, int):
raise TypeError("offset_file argument has to be an integer.")
if not isinstance(buffer_size, int):
raise TypeError("buffer_size argument has to be an integer.")
# read the number of integrals already in the file
integral_num = read_$group_dset$_size(trexio_file)
# additional modification needed to avoid allocating more memory than needed if EOF will be reached during read
overflow = offset_file + buffer_size - integral_num
eof_flag = False
if overflow > 0:
verified_size = buffer_size - overflow
eof_flag = True
else:
verified_size = buffer_size
# main call to the low-level (SWIG-wrapped) trexio_read function, which also requires the sizes of the output to be provided
# as the last 2 arguments (for numpy arrays of indices and values, respectively)
# read_buf_size contains the number of elements being read from the file, useful when EOF has been reached
rc, n_int_read, indices, values = pytr.trexio_read_safe_$group_dset$(trexio_file.pytrexio_s,
offset_file,
verified_size,
verified_size * $group_dset_rank$,
verified_size)
if rc != TREXIO_SUCCESS:
raise Error(rc)
if n_int_read == 0:
raise ValueError("No integrals have been read from the file.")
if indices is None or values is None:
raise ValueError("Returned NULL array from the low-level pytrexio API.")
# conversion to custom types can be performed on the user side, here we only reshape the returned flat array of indices according to group_dset_rank
shape = tuple([verified_size, $group_dset_rank$])
indices_reshaped = np.reshape(indices, shape, order='C')
return (indices_reshaped, values, n_int_read, eof_flag)
def read_$group_dset$_size(trexio_file) -> int:
"""Read the number of $group_dset$ integrals stored in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
~num_integral~: int
Integer value of corresponding to the size of the $group_dset$ sparse array from ~trexio_file~.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc, num_integral = pytr.trexio_read_$group_dset$_size(trexio_file.pytrexio_s)
if rc != TREXIO_SUCCESS:
raise Error(rc)
return num_integral
#+end_src
#+begin_src python :tangle has_dset_sparse_front.py
def has_$group_dset$(trexio_file) -> bool:
"""Check that $group_dset$ variable exists in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
True if the variable exists, False otherwise
Raises:
- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_has_$group_dset$(trexio_file.pytrexio_s)
if rc == TREXIO_FAILURE:
raise Error(rc)
return rc == TREXIO_SUCCESS
#+end_src
** Templates for front end has/read/write a dataset of strings
*** Introduction
This section concerns API calls related to datasets of strings.
| Function name | Description |
|-----------------------------+-------------------------------------|
| ~trexio_has_$group_dset$~ | Check if a dataset exists in a file |
| ~trexio_read_$group_dset$~ | Read a dataset |
| ~trexio_write_$group_dset$~ | Write a dataset |
*** C templates for front end
First parameter is the ~TREXIO~ file handle. Second parameter is the variable to be written/read
to/from the ~TREXIO~ file (except for ~trexio_has_~ functions).
**** Function declarations
#+begin_src c :tangle hrw_dset_str_front.h :exports none
trexio_exit_code trexio_has_$group_dset$(trexio_t* const file);
trexio_exit_code trexio_read_$group_dset$_low(trexio_t* const file, char* dset_out, const int32_t max_str_len);
trexio_exit_code trexio_write_$group_dset$_low(trexio_t* const file, char* dset_in, const int32_t max_str_len);
trexio_exit_code trexio_read_$group_dset$(trexio_t* const file, char** dset_out, const int32_t max_str_len);
trexio_exit_code trexio_write_$group_dset$(trexio_t* const file, const char** dset_in, const int32_t max_str_len);
#+end_src
**** Source code for default functions
#+begin_src c :tangle read_dset_str_front.c
trexio_exit_code
trexio_read_$group_dset$_low (trexio_t* const file, char* dset_out, const int32_t max_str_len)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_out == NULL) return TREXIO_INVALID_ARG_2;
if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
uint32_t rank = $group_dset_rank$;
uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_read_$group_dset$(file, dset_out, rank, dims, (uint32_t) max_str_len);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_read_$group_dset$(file, dset_out, rank, dims, (uint32_t) max_str_len);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_read_$group_dset$(file, dset_out, rank, dims);
,*/
}
return TREXIO_FAILURE;
}
trexio_exit_code
trexio_read_$group_dset$ (trexio_t* const file, char** dset_out, const int32_t max_str_len)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_out == NULL) return TREXIO_INVALID_ARG_2;
if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
if (trexio_has_$group_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
assert(file->back_end < TREXIO_INVALID_BACK_END);
trexio_exit_code rc;
int64_t dset_dim = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &(dset_dim));
if (dset_dim == 0L) return TREXIO_INVALID_NUM;
char* str_compiled = CALLOC(dset_dim*(max_str_len+1) + 1, char);
if (str_compiled == NULL) return TREXIO_ALLOCATION_FAILED;
rc = trexio_read_$group_dset$_low(file, str_compiled, max_str_len);
if (rc != TREXIO_SUCCESS) {
FREE(str_compiled);
return rc;
}
for (uint64_t i=0; i < (uint64_t) dset_dim; i++) {
char * pch;
pch = i == 0 ? strtok(str_compiled, TREXIO_DELIM) : strtok(NULL, TREXIO_DELIM) ;
if (pch == NULL) {
FREE(str_compiled);
return TREXIO_FAILURE;
}
strcpy(dset_out[i], "");
strcat(dset_out[i], pch);
}
FREE(str_compiled);
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle write_dset_str_front.c
trexio_exit_code
trexio_write_$group_dset$_low (trexio_t* const file, char* dset_in, const int32_t max_str_len)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
uint32_t rank = $group_dset_rank$;
uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
assert(file->back_end < TREXIO_INVALID_BACK_END);
char* tmp_str = CALLOC(dims[0]*(max_str_len+1), char);
if (tmp_str == NULL) return TREXIO_ALLOCATION_FAILED;
char** dset_str = CALLOC(dims[0], char*);
if (dset_str == NULL) {
FREE(tmp_str);
return TREXIO_ALLOCATION_FAILED;
}
/* parse the string using strtok */
for(uint64_t i=0; i<dims[0]; i++) {
char* pch;
pch = i == 0 ? strtok(dset_in, TREXIO_DELIM) : strtok(NULL, TREXIO_DELIM) ;
if (pch == NULL) {
FREE(dset_str[0]);
FREE(dset_str);
return TREXIO_FAILURE;
}
size_t pch_len = strlen(pch) + 1;
if (pch_len > (size_t) max_str_len) {
FREE(dset_str[0]);
FREE(dset_str);
return TREXIO_INVALID_STR_LEN;
}
dset_str[i] = tmp_str;
strncpy(tmp_str, pch, pch_len);
tmp_str += pch_len + 1;
}
rc = TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_$group_dset$(file, (const char**) dset_str, rank, dims);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_$group_dset$(file, (const char**) dset_str, rank, dims);
break;
#else
rc =TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_write_$group_dset$(file, dset, rank, dims);
break;
,*/
}
FREE(dset_str[0]);
FREE(dset_str);
return rc;
}
trexio_exit_code
trexio_write_$group_dset$ (trexio_t* const file, const char** dset_in, const int32_t max_str_len)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
assert(file->back_end < TREXIO_INVALID_BACK_END);
trexio_exit_code rc;
int64_t dset_dim = 0;
/* Error handling for this call is added by the generator */
rc = trexio_read_$group_dset_dim$_64(file, &(dset_dim));
if (dset_dim == 0L) return TREXIO_INVALID_NUM;
char* str_compiled = CALLOC(dset_dim*max_str_len + 1, char);
if (str_compiled == NULL) return TREXIO_ALLOCATION_FAILED;
strcpy(str_compiled, "");
for (uint64_t i=0; i < (uint64_t) dset_dim; i++) {
strcat(str_compiled, dset_in[i]);
strcat(str_compiled, TREXIO_DELIM);
}
rc = trexio_write_$group_dset$_low(file, str_compiled, max_str_len);
FREE(str_compiled);
return rc;
}
#+end_src
#+begin_src c :tangle has_dset_str_front.c
trexio_exit_code
trexio_has_$group_dset$ (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_has_$group_dset$(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_has_$group_dset$(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_has_$group_dset$(file);
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
*** Fortran templates for front end
The ~Fortran~ templates that provide an access to the ~C~ API calls from ~Fortran~.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle write_dset_str_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_dset$_low (trex_file, dset, max_str_len) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
character(kind=c_char), intent(in) :: dset(*)
integer(c_int32_t), intent(in), value :: max_str_len
end function trexio_write_$group_dset$_low
end interface
#+end_src
#+begin_src f90 :tangle read_dset_str_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_dset$_low (trex_file, dset, max_str_len) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
character(kind=c_char), intent(out) :: dset(*)
integer(c_int32_t), intent(in), value :: max_str_len
end function trexio_read_$group_dset$_low
end interface
#+end_src
#+begin_src f90 :tangle has_dset_str_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_has_$group_dset$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_dset$
end interface
#+end_src
#+begin_src f90 :tangle helper_read_dset_str_front_fortran.fh_90
integer(trexio_exit_code) function trexio_read_$group_dset$ (trex_file, dset, max_str_len)
implicit none
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int32_t), intent(in), value :: max_str_len
character(len=*), intent(inout) :: dset(*)
character, allocatable :: str_compiled(:)
integer(c_int64_t) :: $group_dset_dim$
integer(trexio_exit_code) :: rc
rc = trexio_read_$group_dset_dim$_64(trex_file, $group_dset_dim$)
if (rc /= TREXIO_SUCCESS) trexio_read_$group_dset$ = rc
allocate(str_compiled($group_dset_dim$*(max_str_len+1)+1))
rc = trexio_read_$group_dset$_low(trex_file, str_compiled, max_str_len)
if (rc /= TREXIO_SUCCESS) then
deallocate(str_compiled)
trexio_read_$group_dset$ = rc
else
call trexio_str2strarray(str_compiled, $group_dset_dim$, max_str_len, dset)
deallocate(str_compiled)
trexio_read_$group_dset$ = TREXIO_SUCCESS
endif
end function trexio_read_$group_dset$
#+end_src
#+begin_src f90 :tangle helper_write_dset_str_front_fortran.fh_90
integer(trexio_exit_code) function trexio_write_$group_dset$ (trex_file, dset, max_str_len)
implicit none
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int32_t), intent(in), value :: max_str_len
character(len=*), intent(in) :: dset(*)
character(len=:), allocatable :: str_compiled
integer(c_int64_t) :: $group_dset_dim$
integer(trexio_exit_code) :: rc
rc = trexio_read_$group_dset_dim$_64(trex_file, $group_dset_dim$)
if (rc /= TREXIO_SUCCESS) then
trexio_write_$group_dset$ = rc
else
call trexio_strarray2str(dset, $group_dset_dim$, max_str_len, str_compiled)
trexio_write_$group_dset$ = trexio_write_$group_dset$_low(trex_file, str_compiled, max_str_len)
endif
end function trexio_write_$group_dset$
#+end_src
*** Python templates for front end
#+begin_src python :tangle write_dset_str_front.py
def write_$group_dset$(trexio_file, dset_w: list) -> None:
"""Write the $group_dset$ array of strings in the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
dset_w: list
Array of $group_dset$ strings to be written.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
max_str_length = len(max(dset_w, key=len)) + 1
rc = pytr.trexio_write_$group_dset$(trexio_file.pytrexio_s, dset_w, max_str_length)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
#+begin_src python :tangle read_dset_str_front.py
def read_$group_dset$(trexio_file, dim = None) -> list:
"""Read the $group_dset$ array of strings from the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
dim (Optional): int
Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
If None, the function will read all necessary array dimensions from the file.
Returns:
~dset_r~: list
1D list with ~dim~ elements corresponding to $group_dset$ strings read from the TREXIO file.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
# if dim is not specified, read dimensions from the TREXIO file
if dim is None:
$group_dset_dim$ = read_$group_dset_dim$(trexio_file)
dims_list = [$group_dset_dim_list$]
dim = 1
for i in range($group_dset_rank$):
dim *= dims_list[i]
rc, dset_1d_r = pytr.trexio_read_$group_dset$_low(trexio_file.pytrexio_s, PYTREXIO_MAX_STR_LENGTH)
if rc != TREXIO_SUCCESS:
raise Error(rc)
dset_full = dset_1d_r.split(pytr.TREXIO_DELIM)
dset_2d_r = [dset_full[i] for i in range(dim) if dset_full[i]]
if not dset_2d_r:
raise ValueError(f"Output of {read_$group_dset$.__name__} function cannot be an empty list.")
return dset_2d_r
#+end_src
#+begin_src python :tangle has_dset_str_front.py
def has_$group_dset$(trexio_file) -> bool:
"""Check that $group_dset$ variable exists in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
True if the variable exists, False otherwise
Raises:
- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_has_$group_dset$(trexio_file.pytrexio_s)
if rc == TREXIO_FAILURE:
raise Error(rc)
return rc == TREXIO_SUCCESS
#+end_src
** Templates for front end has/read/write a single string attribute
*** Introduction
This section concerns API calls related to string attributes.
| Function name | Description |
|----------------------------+----------------------------------------------|
| ~trexio_has_$group_str$~ | Check if a string attribute exists in a file |
| ~trexio_read_$group_str$~ | Read a string attribute |
| ~trexio_write_$group_str$~ | Write a string attribute |
*** C templates for front end
**** Function declarations
#+begin_src c :tangle hrw_attr_str_front.h :exports none
trexio_exit_code trexio_has_$group_str$(trexio_t* const file);
trexio_exit_code trexio_read_$group_str$(trexio_t* const file, char* const str_out, const int32_t max_str_len);
trexio_exit_code trexio_write_$group_str$(trexio_t* const file, const char* str, const int32_t max_str_len);
#+end_src
**** Source code for default functions
#+begin_src c :tangle read_attr_str_front.c
trexio_exit_code
trexio_read_$group_str$ (trexio_t* const file, char* const str_out, const int32_t max_str_len)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (str_out == NULL) return TREXIO_INVALID_ARG_2;
if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
if (trexio_has_$group_str$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_read_$group_str$(file, str_out, (uint32_t) max_str_len);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_read_$group_str$(file, str_out, (uint32_t) max_str_len);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_read_$group_str$(file, str);
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
#+begin_src c :tangle write_attr_str_front.c
trexio_exit_code
trexio_write_$group_str$ (trexio_t* const file, const char* str, const int32_t max_str_len)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (str == NULL) return TREXIO_INVALID_ARG_2;
if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
if (trexio_has_$group_str$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
size_t len_write = strlen(str);
if ((size_t) max_str_len < len_write) return TREXIO_INVALID_STR_LEN;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_$group_str$(file, str);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_write_$group_str$(file, str);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_write_$group_str$(file, str);
,*/
}
return TREXIO_FAILURE;
}
#+end_src
#+begin_src c :tangle has_attr_str_front.c
trexio_exit_code
trexio_has_$group_str$ (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_has_$group_str$(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_has_$group_str$(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_has_$group_str$(file);
,*/
}
return TREXIO_FAILURE;
}
#+end_src
*** Fortran templates for front end
The ~Fortran~ templates that provide an access to the ~C~ API calls from Fortran.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle write_attr_str_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_$group_str$_c (trex_file, str, max_str_len) &
bind(C, name="trexio_write_$group_str$")
use, intrinsic :: iso_c_binding
import
integer(trexio_t), intent(in), value :: trex_file
character(kind=c_char), intent(in) :: str(*)
integer(c_int32_t), intent(in), value :: max_str_len
end function trexio_write_$group_str$_c
end interface
#+end_src
#+begin_src f90 :tangle read_attr_str_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_$group_str$_c (trex_file, str, max_str_len) &
bind(C, name="trexio_read_$group_str$")
use, intrinsic :: iso_c_binding
import
integer(trexio_t), intent(in), value :: trex_file
character(kind=c_char), intent(out) :: str(*)
integer(c_int32_t), intent(in), value :: max_str_len
end function trexio_read_$group_str$_c
end interface
#+end_src
#+begin_src f90 :tangle has_attr_str_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_has_$group_str$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(trexio_t), intent(in), value :: trex_file
end function trexio_has_$group_str$
end interface
#+end_src
#+begin_src f90 :tangle helper_read_attr_str_front_fortran.fh_90
integer(trexio_exit_code) function trexio_read_$group_str$ (trex_file, str, max_str_len)
implicit none
integer(trexio_t), intent(in), value :: trex_file
integer(c_int32_t), intent(in), value :: max_str_len
character, intent(out) :: str(*)
trexio_read_$group_str$ = trexio_read_$group_str$_c(trex_file, str, max_str_len)
end function trexio_read_$group_str$
#+end_src
#+begin_src f90 :tangle helper_write_attr_str_front_fortran.fh_90
integer(trexio_exit_code) function trexio_write_$group_str$ (trex_file, str, max_str_len)
use, intrinsic :: iso_c_binding, only : c_null_char
implicit none
integer(trexio_t), intent(in), value :: trex_file
integer(c_int32_t), intent(in), value :: max_str_len
character(len=*), intent(in) :: str
character(len=len_trim(str)+1) :: str_c
str_c = trim(str) // c_null_char
trexio_write_$group_str$ = trexio_write_$group_str$_c(trex_file, str_c, max_str_len)
end function trexio_write_$group_str$
#+end_src
*** Python templates for front end
#+begin_src python :tangle write_attr_str_front.py
def write_$group_str$(trexio_file, str_w: str) -> None:
"""Write the $group_str$ variable in the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
str_w: str
String corresponding to the $group_str$ variable to be written.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
max_str_length = len(str_w) + 1
rc = pytr.trexio_write_$group_str$(trexio_file.pytrexio_s, str_w, max_str_length)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
#+begin_src python :tangle read_attr_str_front.py
def read_$group_str$(trexio_file) -> str:
"""Read the $group_str$ variable from the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
~str_r~: str
String corresponding to the $group_str$ variable read from ~trexio_file~.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc, str_r = pytr.trexio_read_$group_str$(trexio_file.pytrexio_s, PYTREXIO_MAX_STR_LENGTH)
if rc != TREXIO_SUCCESS:
raise Error(rc)
return str_r
#+end_src
#+begin_src python :tangle has_attr_str_front.py
def has_$group_str$(trexio_file) -> bool:
"""Check that $group_str$ variable exists in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
True if the variable exists, False otherwise
Raises:
- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_has_$group_str$(trexio_file.pytrexio_s)
if rc == TREXIO_FAILURE:
raise Error(rc)
return rc == TREXIO_SUCCESS
#+end_src
** Templates for front end delete an entire group (UNSAFE MODE)
*** Introduction
This section concerns API calls related to string attributes.
| Function name | Description |
|-------------------------+-------------------------------------------|
| ~trexio_delete_$group$~ | Delete a given group from the TREXIO file |
*** C templates for front end
#+begin_src c :tangle delete_group_front.h :exports none
trexio_exit_code trexio_delete_$group$(trexio_t* const file);
#+end_src
#+begin_src c :tangle delete_group_front.c
trexio_exit_code
trexio_delete_$group$ (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (file->mode != 'u') return TREXIO_SAFE_MODE;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_delete_$group$(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_delete_$group$(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_delete_$group$(file);
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
*** Fortran templates for front end
The ~Fortran~ templates that provide an access to the ~C~ API calls from Fortran.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle delete_group_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_delete_$group$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(trexio_t), intent(in), value :: trex_file
end function trexio_delete_$group$
end interface
#+end_src
*** Python templates for front end
#+begin_src python :tangle delete_group_front.py
def delete_$group$(trexio_file) -> None:
"""Delete the entire $group$ group from the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_delete_$group$(trexio_file.pytrexio_s)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
* Source code for the determinant part
Storage of the determinants is a particular case,
which requires special treatment, but has to be coded only once
(since there is only one group that corresponds to it).
Thus, there is no need to auto-generate this part via templates.
This section concerns API calls related to Slater determinants.
| Function name | Description |
|--------------------------------------------+----------------------------------------------------|
| ~trexio_has_determinant_coefficient~ | Check if an attribute exists in a file |
| ~trexio_has_determinant_list~ | Check if an attribute exists in a file |
| ~trexio_write_determinant_coefficient~ | Write an attribute |
| ~trexio_write_determinant_list~ | Write an attribute |
| ~trexio_read_determinant_coefficient~ | Read an attribute |
| ~trexio_read_determinant_list~ | Read an attribute |
| ~trexio_read_determinant_coefficient_size~ | Get the number of the coefficients |
| ~trexio_get_int64_num~ | Get the number of int64 bit fields per determinant |
*** C source code
#+begin_src c :tangle hrw_determinant_front.h :exports none
trexio_exit_code trexio_has_determinant_list(trexio_t* const file);
trexio_exit_code trexio_has_determinant_coefficient(trexio_t* const file);
trexio_exit_code trexio_read_determinant_list(trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size, int64_t* const dset);
trexio_exit_code trexio_read_safe_determinant_list(trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size_read, int64_t* const dset_out, const int64_t dim_out);
trexio_exit_code trexio_read_determinant_coefficient(trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size, double* const dset);
trexio_exit_code trexio_read_safe_determinant_coefficient(trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size_read, double* const dset_out, const int64_t dim_out);
trexio_exit_code trexio_write_determinant_list(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int64_t* dset);
trexio_exit_code trexio_write_safe_determinant_list(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int64_t* dset_in, const int64_t dim_in);
trexio_exit_code trexio_write_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const double* dset);
trexio_exit_code trexio_write_safe_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const double* dset_in, const int64_t dim_in);
trexio_exit_code trexio_read_determinant_coefficient_size(trexio_t* const file, int64_t* const size_max);
trexio_exit_code trexio_get_int64_num(trexio_t* const file, int32_t* const num);
#+end_src
#+begin_src c :tangle read_determinant_front.c
trexio_exit_code
trexio_get_int64_num(trexio_t* const file, int32_t* const num)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (num == NULL) return TREXIO_INVALID_ARG_2;
/* Read the number of mos */
int64_t mo_num = 0L;
trexio_exit_code rc = trexio_read_mo_num_64(file, &mo_num);
if (rc != TREXIO_SUCCESS) return rc;
if (mo_num == 0L) return TREXIO_INVALID_NUM;
/* Compute how many integer numbers is needed to represent a determinant */
int32_t int_num = 0;
int_num = (mo_num - 1L)/64 + 1;
*num = int_num;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle read_determinant_front.c
trexio_exit_code
trexio_read_determinant_list (trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size_read, int64_t* const dset)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_determinant_list(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
/* Get the number of int bit fields per determinant */
int32_t int_num = 0;
trexio_exit_code rc = trexio_get_int64_num(file, &int_num);
if (rc != TREXIO_SUCCESS) return rc;
uint32_t rank = 2;
uint64_t det_size = (uint64_t) (*buffer_size_read);
uint64_t dims[2] = {det_size, int_num*2UL};
// introduce a new variable which will be modified with the number of integrals being read if EOF is encountered
int64_t eof_read_size = 0L;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_read_determinant_list(file, offset_file, rank, dims, &eof_read_size, dset);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_read_determinant_list(file, offset_file, rank, dims, &eof_read_size, dset);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
return trexio_json_read_$group_dset$(...);
break;
,*/
default:
rc = TREXIO_FAILURE; /* Impossible case */
break;
}
if (rc != TREXIO_SUCCESS && rc != TREXIO_END) return rc;
if (rc == TREXIO_END) *buffer_size_read = eof_read_size;
return rc;
}
#+end_src
#+begin_src c :tangle read_determinant_front.c
trexio_exit_code
trexio_read_determinant_coefficient (trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size_read, double* const dset)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_determinant_coefficient(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
trexio_exit_code rc;
uint32_t rank = 1;
uint64_t det_size = (uint64_t) (*buffer_size_read);
uint64_t dims[1] = {det_size};
// introduce a new variable which will be modified with the number of integrals being read if EOF is encountered
int64_t eof_read_size = 0L;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_read_determinant_coefficient(file, offset_file, rank, dims, &eof_read_size, dset);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_read_determinant_coefficient(file, offset_file, rank, dims, &eof_read_size, dset);
break;
#else
rc = TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
return trexio_json_read_$group_dset$(...);
break;
,*/
default:
rc = TREXIO_FAILURE; /* Impossible case */
break;
}
if (rc != TREXIO_SUCCESS && rc != TREXIO_END) return rc;
if (rc == TREXIO_END) *buffer_size_read = eof_read_size;
return rc;
}
#+end_src
#+begin_src c :tangle read_determinant_front.c
trexio_exit_code
trexio_read_determinant_coefficient_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_determinant_coefficient(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_read_determinant_coefficient_size(file, size_max);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_read_determinant_coefficient_size(file, size_max);
break;
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_read_
break;
,*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}
#+end_src
#+begin_src c :tangle read_determinant_front.c
trexio_exit_code
trexio_read_safe_determinant_list (trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size_read, int64_t* const dset_out, const int64_t dim_out)
{
return trexio_read_determinant_list(file, offset_file, buffer_size_read, dset_out);
}
trexio_exit_code
trexio_read_safe_determinant_coefficient (trexio_t* const file, const int64_t offset_file, int64_t* const buffer_size_read, double* const dset_out, const int64_t dim_out)
{
return trexio_read_determinant_coefficient(file, offset_file, buffer_size_read, dset_out);
}
#+end_src
#+begin_src c :tangle write_determinant_front.c
trexio_exit_code
trexio_write_determinant_list (trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int64_t* dset)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset == NULL) return TREXIO_INVALID_ARG_2;
/* Get the number of int bit fields per determinant */
int32_t int_num = 0;
trexio_exit_code rc = trexio_get_int64_num(file, &int_num);
if (rc != TREXIO_SUCCESS) return rc;
uint32_t rank = 2;
uint64_t dims[2] = {buffer_size, int_num*2UL};
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_write_determinant_list(file, offset_file, rank, dims, dset);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
rc = trexio_hdf5_write_determinant_list(file, offset_file, rank, dims, dset);
break;
#else
return TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_read_
break;
,*/
}
if (rc != TREXIO_SUCCESS) return rc;
// Update the determinant_num value with the number of determinants written
int64_t det_num = 0L;
// Read the determinant_num if it exists already
if (trexio_has_determinant_num(file) == TREXIO_SUCCESS) {
rc = trexio_read_determinant_num_64(file, &det_num);
if (rc != TREXIO_SUCCESS) return rc;
}
// Check for the INT64 overflow before writing an updated value
if (INT64_MAX - det_num > buffer_size) {
det_num += buffer_size;
} else {
return TREXIO_INT_SIZE_OVERFLOW;
}
// Overwrite previous value. Here we have to temporarily set the file->mode to 'u' to trick the API
// in order to overwrite existing determinant_num. Otherwise the API returns TREXIO_NUM_ALREADY_EXISTS.
char mode_tmp = file->mode;
file->mode = 'u';
rc = trexio_write_determinant_num_64(file, det_num);
file->mode = mode_tmp;
if (rc != TREXIO_SUCCESS) return rc;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle write_determinant_front.c
trexio_exit_code
trexio_write_determinant_coefficient (trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const double* dset)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset == NULL) return TREXIO_INVALID_ARG_2;
uint32_t rank = 1;
uint64_t dims[1] = {buffer_size};
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_determinant_coefficient(file, offset_file, rank, dims, dset);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_write_determinant_coefficient(file, offset_file, rank, dims, dset);
break;
#else
return TREXIO_BACK_END_MISSING;
break;
#endif
/*
case TREXIO_JSON:
rc = trexio_json_read_
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
#+begin_src c :tangle write_determinant_front.c
trexio_exit_code
trexio_write_safe_determinant_list (trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int64_t* dset_in, const int64_t dim_in)
{
return trexio_write_determinant_list(file, offset_file, buffer_size, dset_in);
}
trexio_exit_code
trexio_write_safe_determinant_coefficient (trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const double* dset_in, const int64_t dim_in)
{
return trexio_write_determinant_coefficient(file, offset_file, buffer_size, dset_in);
}
#+end_src
#+begin_src c :tangle has_determinant_front.c
trexio_exit_code
trexio_has_determinant_list (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_has_determinant_list(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_has_determinant_list(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_has_
break;
,*/
}
return TREXIO_FAILURE;
}
trexio_exit_code
trexio_has_determinant_coefficient (trexio_t* const file)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
assert(file->back_end < TREXIO_INVALID_BACK_END);
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_has_determinant_coefficient(file);
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_has_determinant_coefficient(file);
#else
return TREXIO_BACK_END_MISSING;
#endif
/*
case TREXIO_JSON:
return trexio_json_has_
break;
,*/
}
return TREXIO_FAILURE;
}
#+end_src
*** Fortran interface
The ~Fortran~ templates that provide an access to the ~C~ API calls from Fortran.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle write_determinant_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_write_determinant_list (trex_file, &
offset_file, buffer_size, list) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size
integer(c_int64_t), intent(in) :: list(*)
end function trexio_write_determinant_list
end interface
interface
integer(trexio_exit_code) function trexio_write_safe_determinant_list (trex_file, &
offset_file, buffer_size, &
list, list_size) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size
integer(c_int64_t), intent(in) :: list(*)
integer(c_int64_t), intent(in), value :: list_size
end function trexio_write_safe_determinant_list
end interface
interface
integer(trexio_exit_code) function trexio_write_determinant_coefficient(trex_file, &
offset_file, buffer_size, coefficient) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size
real(c_double), intent(in) :: coefficient(*)
end function trexio_write_determinant_coefficient
end interface
interface
integer(trexio_exit_code) function trexio_write_safe_determinant_coefficient (trex_file, &
offset_file, buffer_size, &
coefficient, coefficient_size) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size
real(c_double), intent(in) :: coefficient(*)
integer(c_int64_t), intent(in), value :: coefficient_size
end function trexio_write_safe_determinant_coefficient
end interface
#+end_src
#+begin_src f90 :tangle read_determinant_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_read_determinant_list(trex_file, &
offset_file, buffer_size, list) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size
integer(c_int64_t), intent(out) :: list(*)
end function trexio_read_determinant_list
end interface
interface
integer(trexio_exit_code) function trexio_read_safe_determinant_list (trex_file, &
offset_file, buffer_size, &
list, list_size) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size
integer(c_int64_t), intent(out) :: list(*)
integer(c_int64_t), intent(in), value :: list_size
end function trexio_read_safe_determinant_list
end interface
interface
integer(trexio_exit_code) function trexio_read_safe_determinant_coefficient (trex_file, &
offset_file, buffer_size, &
coefficient, coefficient_size) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size
real(c_double), intent(out) :: coefficient(*)
integer(c_int64_t), intent(in), value :: coefficient_size
end function trexio_read_safe_determinant_coefficient
end interface
interface
integer(trexio_exit_code) function trexio_read_determinant_coefficient(trex_file, &
offset_file, buffer_size, coefficient) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size
real(c_double), intent(out) :: coefficient(*)
end function trexio_read_determinant_coefficient
end interface
interface
integer(trexio_exit_code) function trexio_read_determinant_coefficient_size (trex_file, &
size_max) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(out) :: size_max
end function trexio_read_determinant_coefficient_size
end interface
#+end_src
#+begin_src f90 :tangle has_determinant_front_fortran.f90
interface
integer(trexio_exit_code) function trexio_has_determinant_list (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_determinant_list
end interface
interface
integer(trexio_exit_code) function trexio_has_determinant_coefficient (trex_file) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_determinant_coefficient
end interface
interface
integer(trexio_exit_code) function trexio_get_int64_num (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file
integer(c_int32_t), intent(out) :: num
end function trexio_get_int64_num
end interface
#+end_src
*** Python interface
#+begin_src python :tangle write_determinant_front.py
def write_determinant_list(trexio_file: File, offset_file: int, buffer_size: int, determinants: list) -> None:
"""Write the determinant list in the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
offset_file: int
The number of determinants to be skipped in the file when writing.
buffer_size: int
The number of determinants to write in the file.
determinants: list OR numpy.ndarray
Array of determinant_list to be written. If array data type does not correspond to int64, the conversion is performed.
Raises:
- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
if not isinstance(offset_file, int):
raise TypeError("offset_file argument has to be an integer.")
if not isinstance(buffer_size, int):
raise TypeError("buffer_size argument has to be an integer.")
if not isinstance(determinants, (list, tuple, np.ndarray)):
raise TypeError("determinants argument has to be an array (list, tuple or NumPy ndarray).")
convert = False
flatten = False
if isinstance(determinants, np.ndarray):
# convert to int64 if input determinants are in a different precision
if not determinants.dtype==np.int64:
convert= True
if len(determinants.shape) > 1:
flatten = True
if convert:
dets_64 = np.int64(determinants).flatten()
else:
dets_64 = np.array(determinants, dtype=np.int64).flatten()
else:
if convert:
dets_64 = np.int64(determinants)
else:
# if input array is a multidimensional list or tuple, we have to convert it
try:
# if list is flat - the attempt to compute len() will raise a TypeError
_ = len(determinants[0])
dets_64 = np.array(determinants, dtype=np.int64).flatten()
flatten = True
except TypeError:
pass
if flatten or convert:
rc = pytr.trexio_write_safe_determinant_list(trexio_file.pytrexio_s, offset_file, buffer_size, dets_64)
else:
rc = pytr.trexio_write_safe_determinant_list(trexio_file.pytrexio_s, offset_file, buffer_size, determinants)
if rc != TREXIO_SUCCESS:
raise Error(rc)
def write_determinant_coefficient(trexio_file: File, offset_file: int, buffer_size: int, coefficients: list) -> None:
"""Write the determinant coefficients in the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
offset_file: int
The number of coefficients to be skipped in the file when writing.
buffer_size: int
The number of coefficients to write in the file.
coefficients: list OR numpy.ndarray
Array of determinant_coefficient to be written. If array data type does not correspond to int64, the conversion is performed.
Raises:
- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
if not isinstance(offset_file, int):
raise TypeError("offset_file argument has to be an integer.")
if not isinstance(buffer_size, int):
raise TypeError("buffer_size argument has to be an integer.")
if not isinstance(coefficients, (list, tuple, np.ndarray)):
raise TypeError("coefficients argument has to be an array (list, tuple or NumPy ndarray).")
if isinstance(coefficients, np.ndarray) and not coefficients.dtype==np.float64:
# convert to float64 if input is in a different precision
coefficients_64 = np.float64(coefficients)
rc = pytr.trexio_write_safe_determinant_coefficient(trexio_file.pytrexio_s, offset_file, buffer_size, coefficients_64)
else:
rc = pytr.trexio_write_safe_determinant_coefficient(trexio_file.pytrexio_s, offset_file, buffer_size, coefficients)
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
#+begin_src python :tangle read_determinant_front.py
def read_determinant_list(trexio_file: File, offset_file: int, buffer_size: int) -> tuple:
"""Read determinant_list from the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
offset_file: int
The number of determinants to be skipped in the file when reading.
buffer_size: int
The number of determinants to read from the file.
Returns:
(determinants, n_int_read, eof_flag) tuple where
- determinants are NumPy arrays [numpy.ndarray] with the default int64 precision;
- n_int_read [int] is the number of determinants read from the trexio_file
(either strictly equal to buffer_size or less than buffer_size if EOF has been reached);
- eof_flag [bool] is True when EOF has been reached (i.e. when call to low-level pytrexio API returns TREXIO_END)
False otherwise.
Raises:
- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
if not isinstance(offset_file, int):
raise TypeError("offset_file argument has to be an integer.")
if not isinstance(buffer_size, int):
raise TypeError("buffer_size argument has to be an integer.")
# read the number of determinants already in the file
det_num = read_determinant_num(trexio_file)
# calculate the int_num (number of int bit fields per determinant)
int_num = 2 * get_int64_num(trexio_file)
# additional modification needed to avoid allocating more memory than needed if EOF will be reached during read
overflow = offset_file + buffer_size - det_num
eof_flag = False
if overflow > 0:
verified_size = buffer_size - overflow
eof_flag = True
else:
verified_size = buffer_size
# main call to the low-level (SWIG-wrapped) trexio_read function, which also requires the sizes of the output to be provided
# read_buf_size contains the number of elements being read from the file, useful when EOF has been reached
rc, n_int_read, determinants = pytr.trexio_read_safe_determinant_list(trexio_file.pytrexio_s,
offset_file,
verified_size,
verified_size * int_num)
if rc != TREXIO_SUCCESS:
raise Error(rc)
if n_int_read == 0:
raise ValueError("No integrals have been read from the file.")
if determinants is None:
raise ValueError("Returned NULL array from the low-level pytrexio API.")
# conversion to custom types can be performed on the user side, here we only reshape the returned flat array according to int_num
dets_reshaped = np.reshape(determinants, (verified_size, int_num), order='C')
return (dets_reshaped, n_int_read, eof_flag)
def read_determinant_coefficient(trexio_file: File, offset_file: int, buffer_size: int) -> tuple:
"""Read determinant_coefficient from the TREXIO file.
Parameters:
trexio_file:
TREXIO File object.
offset_file: int
The number of coefficient to be skipped in the file when reading.
buffer_size: int
The number of coefficients to read from the file.
Returns:
(coefficients, n_int_read, eof_flag) tuple where
- coefficients are NumPy arrays [numpy.ndarray] with the default int64 precision;
- n_int_read [int] is the number of coefficients read from the trexio_file
(either strictly equal to buffer_size or less than buffer_size if EOF has been reached);
- eof_flag [bool] is True when EOF has been reached (i.e. when call to low-level pytrexio API returns TREXIO_END)
False otherwise.
Raises:
- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
- Exception from some other error (e.g. RuntimeError).
"""
try:
import numpy as np
except ImportError:
raise Exception("NumPy cannot be imported.")
if not isinstance(offset_file, int):
raise TypeError("offset_file argument has to be an integer.")
if not isinstance(buffer_size, int):
raise TypeError("buffer_size argument has to be an integer.")
# read the number of determinants already in the file
det_num = read_determinant_coefficient_size(trexio_file)
# additional modification needed to avoid allocating more memory than needed if EOF will be reached during read
overflow = offset_file + buffer_size - det_num
eof_flag = False
if overflow > 0:
verified_size = buffer_size - overflow
eof_flag = True
else:
verified_size = buffer_size
# main call to the low-level (SWIG-wrapped) trexio_read function, which also requires the sizes of the output to be provided
# read_buf_size contains the number of elements being read from the file, useful when EOF has been reached
rc, n_int_read, coefficients = pytr.trexio_read_safe_determinant_coefficient(trexio_file.pytrexio_s,
offset_file,
verified_size,
verified_size)
if rc != TREXIO_SUCCESS:
raise Error(rc)
if n_int_read == 0:
raise ValueError("No integrals have been read from the file.")
if coefficients is None:
raise ValueError("Returned NULL array from the low-level pytrexio API.")
return (coefficients, n_int_read, eof_flag)
def read_determinant_coefficient_size(trexio_file) -> int:
"""Read the number of determinant coefficients stored in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
~num~: int
Integer value of corresponding to the size of the determinant_coefficient array from ~trexio_file~.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc, num = pytr.trexio_read_determinant_coefficient_size(trexio_file.pytrexio_s)
if rc != TREXIO_SUCCESS:
raise Error(rc)
return num
def get_int64_num(trexio_file) -> int:
"""Compute the number of int64 bit fields corresponding to the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
~num~: int
Number of int64 bit fields per determinant.
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc, num = pytr.trexio_get_int64_num(trexio_file.pytrexio_s)
if rc != TREXIO_SUCCESS:
raise Error(rc)
return num
#+end_src
#+begin_src python :tangle has_determinant_front.py
def has_determinant_list(trexio_file) -> bool:
"""Check that determinant_list exists in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
True if the variable exists, False otherwise
Raises:
- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_has_determinant_list(trexio_file.pytrexio_s)
if rc == TREXIO_FAILURE:
raise Error(rc)
return rc == TREXIO_SUCCESS
def has_determinant_coefficient(trexio_file) -> bool:
"""Check that determinant_coefficient exists in the TREXIO file.
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
Returns:
True if the variable exists, False otherwise
Raises:
- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
rc = pytr.trexio_has_determinant_coefficient(trexio_file.pytrexio_s)
if rc == TREXIO_FAILURE:
raise Error(rc)
return rc == TREXIO_SUCCESS
#+end_src
* 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) ~HAVE_HDF5~ [bool]
3) ~HDF5_VERSION~ [string] (optional, only if ~HAVE_HDF5~ is ~true~)
4) ~TREXIO_GIT_HASH~ [string]
~trexio_mark_safety~ checks if the file has been open in UNSAFE mode.
If it was, the ~metadata_unsafe~ attribute can be overwritten with the value provided in a second argument of the function.
Since ~metadata_unsafe~ is set to ~1~ (~true~) upon the first opening of the file in UNSAFE mode, this value is immutable.
However, if the user validated that the file is correct (e.g. using ~trexio-tools~),
then value of the ~metadata_unsafe~ attribute can be changed using the aforementioned function.
~trexio_to_orbital_list~ function converts the list of integer bit fields of a
given determinant into a list of indices of the occupied orbitals (for one spin component).
~trexio_to_orbital_list_up_dn~ function does the same but for both up- and down-spin components
of the determinant and returns two list of orbitals each corresponding to a different component.
** C
#+begin_src c :tangle prefix_front.h
trexio_exit_code trexio_info(void);
trexio_exit_code trexio_mark_safety(trexio_t* const file, const int32_t safety_flag);
typedef int64_t bitfield_t;
#define TREXIO_ORBITAL_SHIFT 1
#define TREXIO_INT_SIZE 64
#define TREXIO_NORB_PER_INT ( 8*sizeof(bitfield_t) )
#
trexio_exit_code trexio_to_orbital_list (const int32_t N_int, const bitfield_t* d1, int32_t* const list, int32_t* const occupied_num);
trexio_exit_code trexio_to_orbital_list_up_dn (const int32_t N_int, const bitfield_t* d1, int32_t* const list_up, int32_t* const list_dn, int32_t* const occ_num_up, int32_t* const occ_num_dn);
trexio_exit_code trexio_safe_to_orbital_list (const int32_t N_int, const bitfield_t* dset_in, const int64_t dim_in, int32_t* const dset_out, const int64_t dim_out, int32_t* const num);
trexio_exit_code trexio_safe_to_orbital_list_up_dn (const int32_t N_int, const bitfield_t* dset_in, const int64_t dim_in, int32_t* const dset_up_out, const int64_t dim_up_out, int32_t* const dset_dn_out, const int64_t dim_dn_out, int32_t* const num_up, int32_t* const num_dn);
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code trexio_to_orbital_list(const int32_t N_int,
const bitfield_t* d1,
int32_t* const list,
int32_t* const occupied_num)
{
if (N_int <= 0) return TREXIO_INVALID_ARG_1;
if (d1 == NULL) return TREXIO_INVALID_ARG_2;
if (list == NULL) return TREXIO_INVALID_ARG_3;
if (occupied_num == NULL) return TREXIO_INVALID_ARG_4;
bitfield_t tmp;
int32_t shift;
int32_t k;
int32_t pos;
k = 0;
shift = TREXIO_ORBITAL_SHIFT;
for (int32_t i=0 ; i<N_int ; i++)
{
tmp = d1[i];
while (tmp != (bitfield_t) 0)
{
pos = trailz(tmp);
if (pos < 0) return TREXIO_FAILURE;
list[k] = ( (int32_t) pos) + shift - 1;
tmp ^= ( ((bitfield_t) 1) << pos);
k++;
}
shift += TREXIO_NORB_PER_INT;
}
,*occupied_num = (int32_t) k;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code trexio_to_orbital_list_up_dn(const int32_t N_int,
const bitfield_t* d1,
int32_t* const list_up,
int32_t* const list_dn,
int32_t* const occ_num_up,
int32_t* const occ_num_dn)
{
if (N_int <= 0) return TREXIO_INVALID_ARG_1;
if (d1 == NULL) return TREXIO_INVALID_ARG_2;
if (list_up == NULL) return TREXIO_INVALID_ARG_3;
if (list_dn == NULL) return TREXIO_INVALID_ARG_4;
if (occ_num_up == NULL) return TREXIO_INVALID_ARG_5;
if (occ_num_dn == NULL) return TREXIO_INVALID_ARG_6;
trexio_exit_code rc;
/* First process up-spin electrons */
rc = trexio_to_orbital_list(N_int, &d1[0], list_up, occ_num_up);
if (rc != TREXIO_SUCCESS) return rc;
/* Now process down-spin electrons */
rc = trexio_to_orbital_list(N_int, &d1[N_int], list_dn, occ_num_dn);
if (rc != TREXIO_SUCCESS) return rc;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_safe_to_orbital_list (const int32_t N_int,
const bitfield_t* dset_in,
const int64_t dim_in,
int32_t* const dset_out,
const int64_t dim_out,
int32_t* const num)
{
return trexio_to_orbital_list(N_int, dset_in, dset_out, num);
}
trexio_exit_code
trexio_safe_to_orbital_list_up_dn (const int32_t N_int,
const bitfield_t* dset_in,
const int64_t dim_in,
int32_t* const dset_up_out,
const int64_t dim_up_out,
int32_t* const dset_dn_out,
const int64_t dim_dn_out,
int32_t* const num_up,
int32_t* const num_dn)
{
return trexio_to_orbital_list_up_dn(N_int, dset_in, dset_up_out, dset_dn_out, num_up, num_dn);
}
#+end_src
#+begin_src c :tangle trexio_private.h
/* Popcount and trailz */
#if TREXIO_INT_SIZE == 64
extern int __builtin_popcountll (unsigned long long x_0);
#define popcnt(X) __builtin_popcountll((unsigned long long) X)
extern int __builtin_ctzll (unsigned long long x_0);
#define trailz(X) __builtin_ctzll((unsigned long long) X)
#elif TREXIO_INT_SIZE == 32
extern int __builtin_popcountl (unsigned long x_0);
#define popcnt(X) __builtin_popcountl((unsigned long) X)
extern int __builtin_ctzl(unsigned long x_0);
#define trailz(X) __builtin_ctzl((unsigned long) X)
#elif TREXIO_INT_SIZE == 16
extern int __builtin_popcount (unsigned int x_0);
#define popcnt(X) __builtin_popcount((unsigned int) X)
extern int __builtin_ctz (unsigned int x_0);
#define trailz(X) __builtin_ctz((unsigned int) X)
#else
#error("Invalid TREXIO_INT_SIZE")
#endif
#+end_src
#+begin_src c :tangle prefix_front.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;
}
#+end_src
#+begin_src c :tangle prefix_front.c
trexio_exit_code
trexio_mark_safety (trexio_t* const file, const int32_t safety_flag)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
/* 1 for true ; 0 for false */
if (safety_flag != 0 && safety_flag != 1) return TREXIO_INVALID_ARG_2;
/* Cannot mark the file in safe mode */
if (file->mode != 'u') return TREXIO_FAILURE;
return trexio_write_metadata_unsafe(file, safety_flag);
}
#+end_src
** Fortran
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer function trexio_info () bind(C)
use, intrinsic :: iso_c_binding
end function trexio_info
end interface
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_to_orbital_list_c(N_int, d1, list, occupied_num) bind(C, name="trexio_to_orbital_list")
use, intrinsic :: iso_c_binding
import
integer(c_int32_t), intent(in), value :: N_int
integer(c_int64_t), intent(in) :: d1(*)
integer(c_int32_t), intent(inout) :: list(*)
integer(c_int32_t), intent(inout) :: occupied_num
end function trexio_to_orbital_list_c
end interface
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90
interface
integer(trexio_exit_code) function trexio_to_orbital_list_up_dn_c(N_int, d1, list_up, list_dn, occ_num_up, occ_num_dn) &
bind(C, name="trexio_to_orbital_list_up_dn")
use, intrinsic :: iso_c_binding
import
integer(c_int32_t), intent(in), value :: N_int
integer(c_int64_t), intent(in) :: d1(*)
integer(c_int32_t), intent(inout) :: list_up(*)
integer(c_int32_t), intent(inout) :: list_dn(*)
integer(c_int32_t), intent(inout) :: occ_num_up
integer(c_int32_t), intent(inout) :: occ_num_dn
end function trexio_to_orbital_list_up_dn_c
end interface
#+end_src
** Python
#+begin_src python :tangle basic_python.py
def info():
"""Print the info about the installed TREXIO library."""
rc = pytr.trexio_info()
if rc != TREXIO_SUCCESS:
raise Error(rc)
#+end_src
#+begin_src python :tangle basic_python.py
def to_orbital_list(n_int: int, determinant: list) -> list:
"""Convert a given determinant into a list of occupied orbitals.
Input:
~determinant~ - list of bit fields (integers)
~n_int~ - number of bit fields per determinant of a given spin
Returns:
~orbital_list~: list
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
# max possible size of the orbital list per spin component (upper limit on the number of MOs)
size_max = n_int * 64
rc, orbital_list, occ_num = pytr.trexio_safe_to_orbital_list(n_int, determinant, size_max)
if rc != TREXIO_SUCCESS:
raise Error(rc)
if len(orbital_list) < occ_num:
raise Exception("Inconsistent size of the orbital_list.")
return orbital_list[0:occ_num]
def to_orbital_list_up_dn(n_int: int, determinant: list) -> tuple:
"""Convert a given determinant into two lists of occupied orbitals.
Input:
~determinant~ - list of bit fields (integers)
~n_int~ - number of bit fields per determinant of a given spin
Returns:
result: tuple with the following items:
~orbital_list_up~: list of orbitals occupied by up-spin electrons
~orbital_list_dn~: list of orbitals occupied by down-spin electrons
Raises:
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
- Exception from some other error (e.g. RuntimeError).
"""
# max possible size of the orbital list per spin component (upper limit on the number of MOs)
size_max = n_int * 64
rc, orbital_list_up, orbital_list_dn, occ_num_up, occ_num_dn = pytr.trexio_safe_to_orbital_list_up_dn(n_int, determinant, size_max, size_max)
if rc != TREXIO_SUCCESS:
raise Error(rc)
if len(orbital_list_up) < occ_num_up:
raise Exception("Inconsistent size of the orbital_list for up-spin electrons.")
if len(orbital_list_dn) < occ_num_dn:
raise Exception("Inconsistent size of the orbital_list for down-spin electrons.")
return (orbital_list_up[0:occ_num_up], orbital_list_dn[0:occ_num_dn])
#+end_src
* 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.
Note, that Fortran interface calls the main ~TREXIO~ API, which is written in C.
#+begin_src f90 :tangle helper_fortran.f90
contains
integer(trexio_t) function trexio_open (filename, mode, back_end, rc_open)
use, intrinsic :: iso_c_binding, only : c_null_char
implicit none
character(len=*), intent(in) :: filename
character, intent(in), value :: mode
integer(trexio_back_end_t), intent(in), value :: back_end
integer(trexio_exit_code), intent(out) :: rc_open
character(len=len_trim(filename)+1) :: filename_c
integer(trexio_exit_code) :: rc
filename_c = trim(filename) // c_null_char
trexio_open = trexio_open_c(filename_c, mode, back_end, rc_open)
if (trexio_open == 0_8 .or. rc_open /= TREXIO_SUCCESS) then
return
endif
rc = trexio_set_one_based(trexio_open)
if (rc /= TREXIO_SUCCESS) then
rc = trexio_close(trexio_open)
trexio_open = 0_8
endif
end function trexio_open
#+end_src
The function below adapts the original C-based ~trexio_inquire~ for Fortran.
This is needed due to the same reasons as for ~trexio_open~ function.
Note, that Fortran interface calls the main ~TREXIO~ API, which is written in C.
#+begin_src f90 :tangle helper_fortran.f90
integer(trexio_exit_code) function trexio_inquire (filename)
use, intrinsic :: iso_c_binding
implicit none
character(len=*), intent(in) :: filename
character(len=len_trim(filename)+1) :: filename_c
filename_c = trim(filename) // c_null_char
trexio_inquire = trexio_inquire_c(filename_c)
end function trexio_inquire
#+end_src
The subroutines below wrap the ~to_orbital_list~ functions to shift the MO indices
by 1 since in Fortran arrays are 1-based and C/Python they are 0-based.
#+begin_src f90 :tangle helper_fortran.f90
integer(trexio_exit_code) function trexio_to_orbital_list(N_int, d1, list, occupied_num)
use, intrinsic :: iso_c_binding
implicit none
integer(c_int32_t), intent(in), value :: N_int
integer(c_int64_t), intent(in) :: d1(*)
integer(c_int32_t), intent(out) :: list(*)
integer(c_int32_t), intent(out) :: occupied_num
integer :: i
trexio_to_orbital_list = trexio_to_orbital_list_c(N_int, d1, list, occupied_num)
if (trexio_to_orbital_list /= TREXIO_SUCCESS) then
return
endif
do i = 1,occupied_num
list(i) = list(i) + 1
enddo
end function trexio_to_orbital_list
integer(trexio_exit_code) function trexio_to_orbital_list_up_dn(N_int, d1, list_up, list_dn, occ_num_up, occ_num_dn)
use, intrinsic :: iso_c_binding
implicit none
integer(c_int32_t), intent(in), value :: N_int
integer(c_int64_t), intent(in) :: d1(*)
integer(c_int32_t), intent(out) :: list_up(*)
integer(c_int32_t), intent(out) :: list_dn(*)
integer(c_int32_t), intent(out) :: occ_num_up
integer(c_int32_t), intent(out) :: occ_num_dn
integer :: i
trexio_to_orbital_list_up_dn = trexio_to_orbital_list_up_dn_c(N_int, d1, list_up, list_dn, occ_num_up, occ_num_dn)
if (trexio_to_orbital_list_up_dn /= TREXIO_SUCCESS) then
return
endif
do i = 1,occ_num_up
list_up(i) = list_up(i) + 1
enddo
do i = 1,occ_num_dn
list_dn(i) = list_dn(i) + 1
enddo
end function trexio_to_orbital_list_up_dn
#+end_src
The subroutine below transforms an array of Fortran strings into one big string using ~TREXIO_DELIM~ symbol
as a delimeter and adds ~NULL~ character in the end in order to properly pass the desired string to
C API. This is needed due to the fact that strings in C are terminated by ~NULL~ character ~\0~.
#+begin_src f90 :tangle helper_fortran.f90
subroutine trexio_strarray2str(str_array, max_num_str, max_len_str, str_res)
use, intrinsic :: iso_c_binding, only : c_null_char
implicit none
integer(c_int64_t), intent(in), value :: max_num_str ! number of elements in strign array
integer, intent(in), value :: max_len_str ! maximum length of a string in an array
character(len=*), intent(in) :: str_array(*)
character(len=:), allocatable, intent(out) :: str_res
integer(c_int64_t) :: i
str_res = ''
do i = 1, max_num_str
str_res = str_res // trim(str_array(i)) // TREXIO_DELIM
enddo
str_res = str_res // c_null_char
end subroutine trexio_strarray2str
#+end_src
The subroutine below does the reverse tranformation from one big string with delimeters into an array of Fortran strings.
#+begin_src f90 :tangle helper_fortran.f90
subroutine trexio_str2strarray(str_flat, max_num_str, max_len_str, str_array)
implicit none
integer(c_int64_t), intent(in), value :: max_num_str ! number of elements in strign array
integer, intent(in), value :: max_len_str ! maximum length of a string in an array
character(kind=c_char), intent(in) :: str_flat(*)
character(len=*), intent(inout) :: str_array(*)
character(len=max_len_str) :: tmp_str
integer(c_int64_t) :: i, j, k, ind, len_flat
len_flat = (max_len_str+1)*max_num_str + 1
ind=1
do i=1,max_num_str
k = 1
tmp_str=''
do j=ind,len_flat
if (str_flat(j) == TREXIO_DELIM) then
ind=j+1
exit
endif
tmp_str(k:k) = str_flat(j)
k = k + 1
enddo
str_array(i)=tmp_str
enddo
end subroutine trexio_str2strarray
#+end_src
The subroutine is a Fortran analogue of ~assert~ in C. It check that the the return code of the
TREXIO API call is equal to a given return code. It can optionally print a success message if the
two code are identical, i.e. if the ~assert~ statement pass.
#+begin_src f90 :tangle helper_fortran.f90
subroutine trexio_assert(trexio_rc, check_rc, success_message)
implicit none
integer, intent(in), value :: trexio_rc
integer, intent(in), value :: check_rc
character(len=*), intent(in), optional :: success_message
character*(128) :: str
if (trexio_rc == check_rc) then
if (present(success_message)) write(*,*) success_message
else
call trexio_string_of_error(trexio_rc, str)
print *, trim(str)
stop 1
endif
end subroutine trexio_assert
#+end_src
* File suffixes :noexport:
#+begin_src c :tangle suffix_front.h
#endif
#+end_src
#+begin_src c :tangle suffix_s_front.h
#endif
#+end_src
#+begin_src f90 :tangle suffix_fortran.f90
end module trexio
#+end_src
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