mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-24 22:21:43 +02:00
Merge branch 'master' into add-determinants
This commit is contained in:
commit
33838546c7
14
Makefile.am
14
Makefile.am
@ -118,7 +118,8 @@ TESTS_C = \
|
||||
tests/io_dset_str_text \
|
||||
tests/delete_group_text \
|
||||
tests/overwrite_all_text \
|
||||
tests/io_all
|
||||
tests/io_all \
|
||||
tests/pre_close
|
||||
|
||||
if HAVE_HDF5
|
||||
TESTS_C += \
|
||||
@ -254,10 +255,15 @@ $(pytrexio_py): $(pytrexio_c)
|
||||
# Build Python module and C wrapper code for TREXIO using SWIG
|
||||
# [?] swig -python -threads pytrexio.i ----> Add thread support for all the interface
|
||||
$(pytrexio_c): $(ORG_FILES) $(GENERATOR_FILES) $(trexio_h) $(pytrexio_i) $(numpy_i)
|
||||
cp $(trexio_h) src/
|
||||
@if [[ $(SWIG).x != ".x" ]] ; then \
|
||||
cp $(trexio_h) src/ ; \
|
||||
cd src/ && \
|
||||
$(SWIG) -python -py3 -o pytrexio_wrap.c pytrexio.i
|
||||
$(RM) -- src/trexio.h
|
||||
$(SWIG) -python -py3 -o pytrexio_wrap.c pytrexio.i ; \
|
||||
$(RM) -- src/trexio.h ;\
|
||||
else echo "Error: SWIG is not installed" ; \
|
||||
exit 1 ; \
|
||||
fi
|
||||
|
||||
|
||||
$(numpy_i):
|
||||
wget https://raw.githubusercontent.com/numpy/numpy/main/tools/swig/numpy.i -O $(numpy_i)
|
||||
|
@ -8,7 +8,7 @@
|
||||
#+INFOJS_OPT: toc:t mouse:underline path:org-info.js
|
||||
#+HTML_HEAD: <link rel="stylesheet" title="Standard" href="trexio.css" type="text/css" />
|
||||
|
||||
#+STARTUP: align fold nodlcheck hidestars oddeven lognotestate
|
||||
#+STARTUP: align nodlcheck hidestars oddeven lognotestate
|
||||
#+AUTHOR: TREX-CoE
|
||||
#+LANGUAGE: en
|
||||
|
||||
|
@ -888,19 +888,17 @@ trexio_open(const char* file_name, const char mode,
|
||||
/* Try to determine the applicable backend if the back_end argument is TREXIO_AUTO */
|
||||
if (back_end == TREXIO_AUTO && mode == 'r') {
|
||||
#ifdef HAVE_HDF5
|
||||
trexio_exit_code rc_text, rc_hdf5;
|
||||
/* Check if the TREXIO file exists and if it is a directory */
|
||||
rc_text = trexio_text_inquire(file_name);
|
||||
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 */
|
||||
rc_hdf5 = trexio_hdf5_inquire(file_name);
|
||||
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 */
|
||||
back_end_local = -1;
|
||||
if (rc_open != NULL) *rc_open = TREXIO_FILE_ERROR;
|
||||
return NULL;
|
||||
}
|
||||
@ -1236,6 +1234,10 @@ trexio_close (trexio_t* file)
|
||||
|
||||
assert(file->back_end < TREXIO_INVALID_BACK_END);
|
||||
|
||||
/* Things to be done before the 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) {
|
||||
|
||||
@ -1478,6 +1480,82 @@ end interface
|
||||
|
||||
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;
|
||||
|
||||
{ /* Up-spin and down-spin electrons */
|
||||
trexio_exit_code rc;
|
||||
|
||||
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 (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) {
|
||||
nelec = nup + ndn;
|
||||
rc = trexio_write_electron_num(file, nelec);
|
||||
if (rc != TREXIO_SUCCESS) return rc;
|
||||
}
|
||||
} 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
|
||||
|
||||
|
@ -439,7 +439,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
|
||||
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
|
||||
|
||||
hid_t index_dtype;
|
||||
void* index_p = NULL;
|
||||
const void* index_p;
|
||||
uint64_t size_ranked = (uint64_t) size * $group_dset_rank$;
|
||||
/* Determine the optimal type for storing indices depending on the size_max (usually mo_num or ao_num) */
|
||||
if (size_max < UINT8_MAX) {
|
||||
@ -459,7 +459,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
|
||||
index_p = index;
|
||||
index_dtype = H5T_NATIVE_UINT16;
|
||||
} else {
|
||||
index_p = (int32_t*) index_sparse;
|
||||
index_p = (const int32_t*) index_sparse;
|
||||
index_dtype = H5T_NATIVE_INT32;
|
||||
}
|
||||
|
||||
|
@ -14,6 +14,7 @@ set(Tests_text
|
||||
io_str_text
|
||||
delete_group_text
|
||||
overwrite_all_text
|
||||
pre_close
|
||||
)
|
||||
|
||||
if(ENABLE_HDF5)
|
||||
|
124
tests/pre_close.c
Normal file
124
tests/pre_close.c
Normal file
@ -0,0 +1,124 @@
|
||||
#include "trexio.h"
|
||||
#include <assert.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <stdint.h>
|
||||
|
||||
#define TEST_BACKEND TREXIO_TEXT
|
||||
#define TREXIO_FILE "test_dset_sparse.dir"
|
||||
#define RM_COMMAND "rm -rf " TREXIO_FILE
|
||||
|
||||
static int test_pre_close_1 (const char* file_name, const back_end_t backend)
|
||||
{
|
||||
/* Check if nelec = nup + ndn */
|
||||
|
||||
trexio_t* file = NULL;
|
||||
trexio_exit_code rc;
|
||||
|
||||
/*================= START OF TEST ==================*/
|
||||
|
||||
// open file in 'write' mode
|
||||
file = trexio_open(file_name, 'w', backend, &rc);
|
||||
assert (file != NULL);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
// write parameters
|
||||
int32_t nup = 4;
|
||||
int32_t ndn = 3;
|
||||
int32_t nelec = 0;
|
||||
|
||||
rc = trexio_write_electron_up_num(file, nup);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
rc = trexio_write_electron_dn_num(file, ndn);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
// close file
|
||||
rc = trexio_close(file);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
|
||||
// re-open file
|
||||
file = trexio_open(file_name, 'r', backend, &rc);
|
||||
assert (file != NULL);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
rc = trexio_read_electron_num(file, &nelec);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
printf("nup : %d\n", nup);
|
||||
printf("ndn : %d\n", ndn);
|
||||
printf("nelec: %d\n", nelec);
|
||||
assert (nelec == nup + ndn);
|
||||
|
||||
// close file
|
||||
rc = trexio_close(file);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
/*================= END OF TEST ==================*/
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int test_pre_close_2 (const char* file_name, const back_end_t backend)
|
||||
{
|
||||
/* Check if nelec = nup */
|
||||
|
||||
trexio_t* file = NULL;
|
||||
trexio_exit_code rc;
|
||||
|
||||
/*================= START OF TEST ==================*/
|
||||
|
||||
// open file in 'write' mode
|
||||
file = trexio_open(file_name, 'w', backend, &rc);
|
||||
assert (file != NULL);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
// write parameters
|
||||
int32_t nup = 4;
|
||||
int32_t nelec = 0;
|
||||
|
||||
rc = trexio_write_electron_up_num(file, nup);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
// close file
|
||||
rc = trexio_close(file);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
|
||||
// re-open file
|
||||
file = trexio_open(file_name, 'r', backend, &rc);
|
||||
assert (file != NULL);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
rc = trexio_read_electron_num(file, &nelec);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
assert (nelec == nup);
|
||||
|
||||
// close file
|
||||
rc = trexio_close(file);
|
||||
assert (rc == TREXIO_SUCCESS);
|
||||
|
||||
/*================= END OF TEST ==================*/
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
int main()
|
||||
{
|
||||
/*============== Test launcher ================*/
|
||||
|
||||
int rc;
|
||||
rc = system(RM_COMMAND);
|
||||
assert (rc == 0);
|
||||
|
||||
test_pre_close_1 (TREXIO_FILE, TEST_BACKEND);
|
||||
rc = system(RM_COMMAND);
|
||||
|
||||
test_pre_close_2 (TREXIO_FILE, TEST_BACKEND);
|
||||
|
||||
rc = system(RM_COMMAND);
|
||||
assert (rc == 0);
|
||||
|
||||
return 0;
|
||||
}
|
54
trex.org
54
trex.org
@ -5,14 +5,10 @@
|
||||
This page contains information about the general structure of the
|
||||
TREXIO library. The source code of the library can be automatically
|
||||
generated based on the contents of the ~trex.json~ configuration file,
|
||||
which itself is compiled from different sections (groups) presented
|
||||
which itself is generated from different sections (groups) presented
|
||||
below.
|
||||
|
||||
For more information about the automatic generation on the source code
|
||||
or regarding possible modifications, please contact the TREXIO
|
||||
developers.
|
||||
|
||||
All quantities are saved in TREXIO file in atomic units. The
|
||||
All quantities are saved in TREXIO files in atomic units. The
|
||||
dimensions of the arrays in the tables below are given in column-major
|
||||
order (as in Fortran), and the ordering of the dimensions is reversed
|
||||
in the produced ~trex.json~ configuration file as the library is
|
||||
@ -21,19 +17,21 @@ written in C.
|
||||
TREXIO currently supports ~int~, ~float~ and ~str~ types for both
|
||||
single attributes and arrays. Note, that some attributes might have
|
||||
~dim~ type (e.g. ~num~ of the ~nucleus~ group). This type is treated
|
||||
exactly the same as ~int~ with the only difference that ~dim~
|
||||
exactly in the same way as ~int~ with the only difference that ~dim~
|
||||
variables cannot be negative. This additional constraint is required
|
||||
because ~dim~ attributes are used internally to allocate memory and to
|
||||
check array boundaries in the memory-safe API. Most of the times, the
|
||||
~dim~ variables contain the ~num~ suffix.
|
||||
|
||||
In Fortran, the arrays are 1-based and in most other languages the
|
||||
arrays are 0-based. Hence, we introduce the ~index~ type which is an
|
||||
In Fortran, arrays are 1-based and in most other languages the
|
||||
arrays are 0-based. Hence, we introduce the ~index~ type which is a
|
||||
1-based ~int~ in the Fortran interface and 0-based otherwise.
|
||||
|
||||
For sparse data structures such as electron replusion integrals,
|
||||
the data can be too large to fit in memory and the data needs to be
|
||||
fetched using multiple function calls to perform I/O on buffers.
|
||||
For more information on how to read/write sparse data structures, see
|
||||
the [[./examples.html][examples]].
|
||||
|
||||
|
||||
#+begin_src python :tangle trex.json :exports none
|
||||
@ -88,6 +86,7 @@ fetched using multiple function calls to perform I/O on buffers.
|
||||
#+NAME:electron
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|----------+-------+------------+-------------------------------------|
|
||||
| ~num~ | ~dim~ | | Number of electrons |
|
||||
| ~up_num~ | ~int~ | | Number of \uparrow-spin electrons |
|
||||
| ~dn_num~ | ~int~ | | Number of \downarrow-spin electrons |
|
||||
|
||||
@ -96,7 +95,8 @@ fetched using multiple function calls to perform I/O on buffers.
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"electron": {
|
||||
"up_num" : [ "int", [] ]
|
||||
"num" : [ "dim", [] ]
|
||||
, "up_num" : [ "int", [] ]
|
||||
, "dn_num" : [ "int", [] ]
|
||||
} ,
|
||||
#+end_src
|
||||
@ -756,7 +756,7 @@ prim_factor =
|
||||
| ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix |
|
||||
| ~2e_dnup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\uparrow component of the two-body reduced density matrix |
|
||||
|
||||
#+CALL: json(data=rdm, title="rdm", last=1)
|
||||
#+CALL: json(data=rdm, title="rdm")
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
@ -770,6 +770,38 @@ prim_factor =
|
||||
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||
, "2e_dnup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Quantum Monte Carlo data (qmc group)
|
||||
|
||||
In quantum Monte Carlo calculations, the wave function is evaluated
|
||||
at points of the 3N-dimensional space. Some algorithms require multiple
|
||||
independent /walkers/, so it is possible to store multiple coordinates,
|
||||
as well as some quantities evaluated at those points.
|
||||
|
||||
By convention, the electron coordinates contain first all the electrons
|
||||
of $\uparrow$-spin and then all the $\downarrow$-spin.
|
||||
|
||||
#+name: qmc
|
||||
| Variable | Type | Dimensions | Description |
|
||||
|----------+---------+------------------------------+---------------------------------------|
|
||||
| ~num~ | ~dim~ | | Number of 3N-dimensional points |
|
||||
| ~point~ | ~float~ | ~(3, electron.num, qmc.num)~ | 3N-dimensional points |
|
||||
| ~psi~ | ~float~ | ~(qmc.num)~ | Wave function evaluated at the points |
|
||||
| ~e_loc~ | ~float~ | ~(qmc.num)~ | Local energy evaluated at the points |
|
||||
|
||||
#+CALL: json(data=qmc, title="qmc", last=1)
|
||||
|
||||
#+RESULTS:
|
||||
:results:
|
||||
#+begin_src python :tangle trex.json
|
||||
"qmc": {
|
||||
"num" : [ "dim" , [] ]
|
||||
, "point" : [ "float", [ "qmc.num", "electron.num", "3" ] ]
|
||||
, "psi" : [ "float", [ "qmc.num" ] ]
|
||||
, "e_loc" : [ "float", [ "qmc.num" ] ]
|
||||
}
|
||||
#+end_src
|
||||
:end:
|
||||
|
Loading…
Reference in New Issue
Block a user