q-posev
c4177465bc
Add safe and Fortran APIs for determinants
2022-04-12 16:34:42 +02:00
q-posev
1dc0f0f089
Manually add source code for determinants
2022-04-12 11:49:02 +02:00
q-posev
722453688b
Fix EOF detection for an arbitrary ranked dset
2022-04-12 11:48:21 +02:00
q-posev
4904de5674
Fix bug with broken data offset upon writing
2022-04-12 11:47:07 +02:00
q-posev
738d8de5ca
TEXT back end working
2022-04-12 00:41:57 +02:00
ac41cd6080
Implement HDF5 functions for determinant_list I/O
2022-04-11 16:33:01 +02:00
a3f70336d7
Add calls to HDF5 back end; overwrite determinant_num
2022-04-11 16:32:23 +02:00
7d640b06dd
Reformat
2022-04-11 16:31:45 +02:00
aa47ae4c2e
Working text back end [to test]
2022-04-11 13:13:56 +02:00
q-posev
a2fee3164b
[WIP] text back end
2022-04-11 09:26:54 +02:00
q-posev
e5d6104a63
[WIP] determinants
2022-04-06 18:26:57 +02:00
e43dde90d9
If nelec != nup+ndn, rewrite nelec
2022-03-31 13:55:50 +02:00
15c8e10184
Added test
2022-03-31 13:53:57 +02:00
8262b97104
Merge branch 'walkers' of github.com:TREX-CoE/trexio into walkers
2022-03-31 13:34:41 +02:00
0e75cb42b5
Add support for Python with statement
...
(see PEP 343 for more details)
2022-03-07 14:12:31 +01:00
68d34a0ace
use built-in trexio_text_free_group function for garbage collection
2022-02-14 10:44:04 +01:00
5eb697abcc
[WIP] refactor read_group set of functions to read data in arbitrary order
...
This fix is required to fix backwards compatibility issue of TEXT back end. In the meantime, the custom garbage collector from generator_tools which was deallocating previously allocated memory (datasets and strings) is no longer valid here since the order of allocation can be atrbitrary. This requires a new custom garbage collector, maybe as a separate functions in TEXT back end
2022-02-07 15:57:38 +01:00
999dd2065a
update documentation of the trexio_open function
2022-02-04 11:21:56 +01:00
246847b8d5
Merge branch 'master' into add-auto-backend
2022-01-25 16:24:34 +01:00
a65b22eebb
add TREXIO_AUTO back end for READONLY (r) mode
2022-01-25 14:59:51 +01:00
4e5bb5472a
remove merge leftovers
2022-01-25 13:17:49 +01:00
dcdac7dbf9
add metadata_unsafe attribute to trex.json; write it upon first unsafe trexio_open
2022-01-25 11:13:32 +01:00
8947f6caa7
Merge branch 'master' into add-unsafe-open-mode
2022-01-24 18:25:52 +01:00
82e7cd058b
add overwriting functionality for unsafe mode [HDF5]
2022-01-24 16:15:31 +01:00
f68a59417e
add overwriting functionality for unsafe mode [TEXT]
2022-01-24 16:13:27 +01:00
179e0c8dfc
document the HDF5 issue with releasing the free space
...
suggest using h5repack after each deletion to get the file size right
2022-01-24 11:52:25 +01:00
6fe5a1eaa7
[WIP] add delete_group functions and unsafe trexio_open mode
2022-01-24 10:10:16 +01:00
Evgeny Posenitskiy
f3d17da7b8
Merge branch 'master' into add-inquire-functionality
2022-01-21 12:33:32 +01:00
734f813544
remove C-kind integer types for TREXIO_VERSION-s in Fortran
2022-01-21 12:28:15 +01:00
3e65a74676
better documentation for trexio_inquire function
2022-01-21 10:07:36 +01:00
2a9cfb3fa4
[CMake] add minor support for pthreads and stdint
2022-01-20 17:32:01 +01:00
4afd9cf2c1
Merge branch 'master' into add-inquire-functionality
2022-01-20 14:32:50 +01:00
23c1601442
add trexio_info function
2022-01-20 14:21:54 +01:00
8817a86cf6
Minor fixes
2022-01-20 11:13:28 +01:00
7cb1ca8d68
add missing checks for NULL pointers
2022-01-20 10:54:22 +01:00
73a8ef1925
Renamed backend -> back_end for consistency + Better type names, using types in functions.
2022-01-20 09:58:27 +01:00
0651ef66b6
Removed erroneous c_double
2022-01-19 22:03:25 +01:00
81c41c1ffc
Merge branch 'master' into iso_fortran_env
2022-01-19 19:45:58 +01:00
78c632f93f
Merge pull request #74 from TREX-CoE/build_fixes
...
Build fixes
2022-01-19 19:33:23 +01:00
e3d1026a41
iso_c_binding
2022-01-19 19:16:03 +01:00
16e9a815d2
Using iso_c_binding types in trexio_f.f90
2022-01-19 19:13:52 +01:00
550c5c3954
implement trexio_inquire function in front and back ends
2022-01-19 14:06:10 +01:00
Pablo Lopez Rios
57973eaca0
templator_front.org: undo two unnecessary changes
2022-01-19 10:38:01 +00:00
Pablo Lopez Rios
9e5d81b292
Use c_int64_t and c_int32_t as requested by Evgeny Posenitskiy.
2022-01-19 10:23:11 +00:00
Pablo Lopez Rios
36a05c184d
Use cmake's configure_file() as suggested by Evgeny Posenitskiy.
2022-01-19 10:14:31 +00:00
Pablo Lopez Rios
0e9b9f1900
trexio_f: fix complaints from gfortran 11, including data type issues
...
This includes:
* Define kind of arguments of bind(C) procedures using the relevant C
types provided by iso_c_binding.
* Replaced "call exit(1)" with "error stop 1".
* Fixed a couple of implicit type conversions between 4-/8-byte
integers.
The first two fix compilation of the Fortran module with -std=f2008.
2022-01-18 16:58:07 +00:00
Pablo Lopez Rios
f89e542f26
gitignore editor swap/backup files, suggested build directory, build byproducts
2022-01-18 14:14:27 +00:00
Pablo Lopez Rios
12a7454c0c
Fix cmake compilation.
...
This includes:
* Declare generated source files in include/ as GENERATED in
TREXIO_DEVEL mode.
* Generate include/config.h with version components from project
delcaration, and for good measure have src/templates_front/build.sh
set version components to 0 if not present.
2022-01-18 14:04:00 +00:00
acff2de611
safer struct
2022-01-07 11:58:24 +01:00
64081e46ad
cppcheck fixes
2022-01-07 11:50:55 +01:00
98e303ffe2
Merge branch 'master' of github.com:TREX-CoE/trexio
2022-01-07 11:22:44 +01:00
3f4b8e2c7e
cppcheck fixes
2022-01-07 11:21:12 +01:00
dbb6f78397
cppcheck fixes
2022-01-07 11:01:23 +01:00
3787226fd1
overlapping changes
2022-01-07 09:58:03 +01:00
1f7386c4ca
Missing break in front end
2022-01-07 08:57:45 +01:00
fc08ee68ef
Merge branch 'master' of github.com:TREX-CoE/trexio
2022-01-05 14:05:25 +01:00
Evgeny Posenitskiy
c687c80f92
Merge pull request #71 from TREX-CoE/add-sparse-datasets
...
Add Python API for sparse datasets
2022-01-05 13:57:32 +01:00
b65ec031dc
rename returned variable to n_int_read
2021-12-27 17:17:00 +01:00
4ef5386ae6
[cppcheck] fix some warnings
2021-12-27 16:29:26 +01:00
6ab5c67ebe
[pre-release] upgrade versions and produce wheels for CPython 3.10
2021-12-27 16:26:17 +01:00
31ffa574ab
finish top-level Python API for sparse data
2021-12-27 14:00:46 +01:00
722c546113
documentation for sparse arrays
...
+ add safe functions to Fortran API
2021-12-24 12:40:23 +01:00
c18a330eab
[WIP] working read/write of sparse data in the low-level (SWIG) Python API
...
TODO: top-level Python API with error handling and truncation of output arrays when EOF is encountered (low-level API fills the remaining elements with garbase)
2021-12-24 11:49:54 +01:00
0a8aa638f6
fix double deallocation in text back end
2021-12-23 18:49:00 +01:00
72897e4b5d
[WIP] read/write of sparse data in Python
2021-12-23 18:27:24 +01:00
c2376bf168
Fixed bug in text back-end when reading empt attributes
2021-12-23 18:21:17 +01:00
q-posev
31ccd27a0a
fix warnings on MacOS
2021-12-17 17:07:53 +01:00
2639b76a6e
optimize storage of indices depending on the size_max variable [TEXT]
2021-12-17 15:32:03 +01:00
daa5bdb3cc
(inout) buffer size instead if (out) [Fortran]
2021-12-17 13:33:27 +01:00
314beb58c9
refactoring done; moved common blocks into _hdf5_open_read_dset_sparse
2021-12-17 13:32:35 +01:00
1c49c81da8
[WIP] refactoring; write_dset_sparse done
2021-12-16 16:52:35 +01:00
fafb155228
return the number of read elements if read_sparse reached EOF
2021-12-16 11:05:57 +01:00
2e99a14b6e
read dim variable of sparse dset to compress storage of indices in HDF5
2021-12-14 18:03:51 +01:00
a8b251d820
write sparse values and compress int indices depending on the max num value
2021-12-14 18:02:58 +01:00
b90abcc307
fix memory leak in the Fortran test
2021-12-13 09:59:27 +01:00
070ef06818
better error handling for HDF5
2021-12-10 16:49:31 +01:00
1c16b75992
adapt HDF5 back end to be generated for an arbitrary number of indices
2021-12-10 16:02:38 +01:00
9f5ee463e1
only shift indices that have been read to the buffer (EOF case)
2021-12-10 14:02:05 +01:00
7afb53be49
implement shift of sparse indices to be one-based in Fortran
2021-12-10 11:34:37 +01:00
e00f3b106e
working HDF5 I/O for sparse indices
2021-12-09 16:13:28 +01:00
e774cb6852
add read_size function to HDF5 back end
2021-12-09 14:10:51 +01:00
d001844c2f
[WIP] working write_ for chunked extensible (sparse) datasets
2021-12-08 17:26:55 +01:00
e5bde10056
alternative way to check for EOF with fgets while reading
2021-12-03 19:23:01 +01:00
ed3bde973e
[WIP] more general templated variables for sparse data
...
+ renamed templated variables with std_dtype_in|out suffix into _format_scanf|printf for clarity
2021-12-03 15:42:40 +01:00
c520175cbe
use size_max values provided by the read_size functions
2021-12-03 11:48:51 +01:00
d2c95cd306
add functions to read the number of stored sparse elements
2021-12-02 17:28:37 +01:00
acdf982a94
fixed string length for file name + comments
2021-12-01 16:28:47 +01:00
7afce779a8
better error handling in TEXT back end
2021-12-01 16:11:40 +01:00
c30c3a532c
add Fortran interface for sparse data
2021-12-01 13:35:42 +01:00
83c926fd6b
replace offset_data arg with pointer arithmetics
2021-12-01 09:56:31 +01:00
d3ba8f3652
[WIP] working generator for sparse functions
...
+ remove trailing whitespaces
2021-11-30 16:30:36 +01:00
c1e1176400
[WIP] text back end
2021-11-24 17:44:54 +01:00
d44883f0ea
add search bar
...
close #40
2021-11-19 12:50:12 +01:00
527417cd8f
fix type conversion for 32-bit indices
2021-11-18 14:33:18 +01:00
72c355c7cc
Top-level CMakeLists with subdirectories
2021-11-17 14:00:35 +01:00
954ee4216c
add trexio_has_backend function to the C and Fortran APIs
2021-11-02 11:05:27 +01:00
7f3ee3cc18
reset back end values and add TREXIO_BACK_END_MISSING error
2021-11-02 10:32:00 +01:00
5504bc0fe6
wrap TREXIO_INVALID_BACK_END definition in preprocessor macro
2021-11-01 13:22:46 +01:00
d42dc7f449
optional HDF5 compilation
...
via configure script and pre-processor macros
2021-11-01 11:55:34 +01:00
1812deb9dd
Check return value of mkdtemp
2021-10-14 10:53:15 +02:00
5cf12131f1
Fix text back end for read-only directories (make distcheck in qmckl)
2021-10-13 17:43:15 +02:00
d017306706
Better error handling with open in text back end
2021-10-13 16:13:24 +02:00
954b26ccff
Update README
2021-10-13 14:24:54 +02:00
fb9c95bd61
add version attributes to the Fortran module
2021-10-08 13:55:56 +02:00
947a8a12f8
Fix bug due to PACKAGE_VERSION definition in trexio.h
2021-10-07 09:54:19 +02:00
68284161d3
downgrade numpy.i SWIG interface to numpy 1.17.3
2021-09-30 17:22:50 +02:00
2e2dac3982
modify rc_open only if it is not a NULL pointer
2021-09-24 12:23:59 +02:00
67b00efa9c
handle return error of trexio_open in the Python API
2021-09-22 16:40:55 +02:00
9457a826d2
return error code from trexio_open [C, Fortran]
2021-09-22 14:50:22 +02:00
14472cda48
better error handling in case of invalid dimensioning variable
2021-09-22 11:33:27 +02:00
389d265f7f
fix cppcheck warnings regarding redundant size_dset_str checks
2021-09-21 16:08:04 +02:00
d1a9af4185
remove blank spaces in front of pointers
2021-09-21 15:54:11 +02:00
788f7e666d
read single numerical attributes based on _isSet bool flag
2021-09-21 15:41:12 +02:00
d5405e700c
raise TREXIO_INVALID_ARG_2 also when writing zero as dimensioning variable
2021-09-21 14:35:29 +02:00
6459543afd
better front end documentation for numerical attributes
2021-09-21 10:58:07 +02:00
11a17c65d3
add attr_ prefix to the template file name for numerical attributes
2021-09-21 10:41:37 +02:00
c22e9d2925
put back sanity check that dimensioning variables are positive
2021-09-20 17:00:05 +02:00
ce0d98b984
add conversion of float-like attributes into an output tuple
2021-09-20 15:52:55 +02:00
4b9827048f
adapt the templates in back ends
2021-09-20 15:51:36 +02:00
261e7c8b84
modify front end for more general numerical attributes
2021-09-20 13:16:44 +02:00
11dadaab36
add tutorial HTML page to the main documentation
2021-09-15 13:43:57 +02:00
f251f0afba
remove unnecessary comments in the SWIG interface
2021-09-14 17:30:05 +02:00
d04106f72d
max_str_len should be int32_t to properly check for negative values
2021-09-13 13:35:45 +02:00
1589995775
do not use warnings for an attempt to overwrite in the Python API
2021-09-13 11:46:31 +02:00
2bd4ef9bfd
add has_ functions to the Python API
2021-09-13 11:29:00 +02:00
77e3f1ac11
print UserWarning instead of raising Error for an attempt to overwrite data
...
following suggestion of Vijay G.C.
2021-09-12 14:24:50 +02:00
d060808467
do not reveal paths to trexio (security concerns)
2021-09-12 13:36:24 +02:00
12dd1fd8dc
apply some suggestions from cppcheck
2021-09-12 13:25:03 +02:00
40d5fc31fc
check that the data object exists before reading it from the file
2021-09-10 09:38:26 +02:00
67e59f156c
explicitly provide __version__ attribute of the trexio module
2021-09-08 19:28:18 +02:00
96678fea2e
adapt write functions to receive multidimensional arrays or lists
2021-09-07 17:14:23 +02:00
3e82fd9ae8
FIX: a bug that was leading to Python and valgrind errors
2021-08-31 12:11:22 +03:00
74c69bb293
better Exception handling with custom exception class
2021-08-30 18:04:35 +03:00
5a2b4d96a7
reshape output arrays by default when reading from the file
2021-08-27 16:08:39 +03:00
7b5ebf6272
implement TREXIO File class and change import of pytrexio module
2021-08-26 17:01:53 +03:00
4c28a4cac8
add type converters for numerical arrays in read/write Python functions
2021-08-26 13:14:46 +03:00
1dcd32ef7d
add SWIG typemaps for safe API calls in single and double precision
2021-08-25 13:31:17 +03:00
ed7e3902e2
add memory-safe functions in single or double precision
2021-08-24 13:32:01 +03:00
2911e91941
make dim an optional argument in read_ functions
...
if dim is None - the function read all necessary dimensions from the TREXIO file
2021-08-24 12:51:43 +03:00
6f7c23aa11
add missing annotations
2021-08-21 13:13:55 +03:00
4fe86ee980
add Python docstrings for API functions
...
+ move definition of Fortran and Python back ends from Constant Prefixes to Back Ends section
2021-08-21 12:47:36 +03:00
5d5025ae1d
get rid of _safe suffix and add dimension to read_dset_str functions
2021-08-20 13:43:15 +03:00
831973fc8e
better python compilation
2021-08-18 16:28:43 +03:00
902147b45b
better structure of the python directory
2021-08-18 15:40:42 +03:00
9cc552409f
rename the front-end Python module
2021-08-18 13:30:03 +03:00
f0bccee32d
single top-level import of pytrexio resolves bug with caching
2021-08-18 13:28:37 +03:00
0b223b9d6e
return type cast of exit codes and back ends in C
...
add top-level string_of_error function in Python
2021-08-14 12:27:11 +03:00
721352cb89
add missing support for reading single string attributes
2021-08-11 16:01:36 +03:00
209f4506c8
update gitignore
2021-08-11 16:01:04 +03:00
2be1abd571
add Python front end
2021-08-11 15:59:58 +03:00
