mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-25 06:31:43 +02:00
commit
16b9e0bcdc
@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
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# Initialize the CMake project.
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project(Trexio
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VERSION 2.3.2
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VERSION 2.4.0
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DESCRIPTION "TREX I/O library"
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LANGUAGES C Fortran
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)
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@ -1,6 +1,12 @@
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CHANGES
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=======
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2.4
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---
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- Added state/energy
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- Made state/id an index instead of an int
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2.3
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---
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@ -2,7 +2,7 @@
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# Process this file with autoconf to produce a configure script.
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AC_PREREQ([2.69])
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AC_INIT([trexio],[2.3.2],[https://github.com/TREX-CoE/trexio/issues])
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AC_INIT([trexio],[2.4.0],[https://github.com/TREX-CoE/trexio/issues])
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AC_CONFIG_SRCDIR([Makefile.in])
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AC_CONFIG_HEADERS([include/config.h])
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@ -1 +1 @@
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__version__ = "1.3.2"
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__version__ = "2.4.0"
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@ -1732,6 +1732,12 @@ def _cp(source: str, destination: str):
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and write it as ~state_id~ attribute.
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~trexio_get_state~ returns current state of the ~trexio_t~ file handle.
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**Warning:** The ~trexio_set_state~ and ~trexio_get_state~ functions still
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use the old convention where the ground state was state ~0~. From version 2.4.0,
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the ~state_id~ variable has changed to ~index~ type, so using the more recent
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~trexio_write_state_id~ and ~trexio_read_state_id~ will give different results
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in Fortran.
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input parameters:
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~file~ -- TREXIO file handle.
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~state~ -- ~int32_t~ ID of a state (0 for ground state).
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@ -2132,24 +2138,35 @@ trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* cons
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if (num == NULL) return TREXIO_INVALID_ARG_2;
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if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
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trexio_exit_code rc = TREXIO_GROUP_READ_ERROR;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_$group_num$(file, num);
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rc = trexio_text_read_$group_num$(file, num);
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break;
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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return trexio_hdf5_read_$group_num$(file, num);
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rc = trexio_hdf5_read_$group_num$(file, num);
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#else
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return TREXIO_BACK_END_MISSING;
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rc = TREXIO_BACK_END_MISSING;
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#endif
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break;
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/*
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case TREXIO_JSON:
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return trexio_json_read_$group_num$(file, num);
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rc = trexio_json_read_$group_num$(file, num);
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break;
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,*/
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}
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return TREXIO_FAILURE;
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if (rc != TREXIO_SUCCESS) return rc;
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/* Handle index type */
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if ($is_index$) {
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,*num += ($group_num_dtype_double$) 1;
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}
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return rc;
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}
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#+end_src
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@ -2161,20 +2178,26 @@ trexio_write_$group_num$_64 (trexio_t* const file, const $group_num_dtype_double
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//if (num <= 0L) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
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if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
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/* Handle index type */
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$group_num_dtype_double$ num_write = num;
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if ($is_index$) {
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num_write -= ($group_num_dtype_double$) 1;
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}
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_write_$group_num$(file, num);
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return trexio_text_write_$group_num$(file, num_write);
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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return trexio_hdf5_write_$group_num$(file, num);
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return trexio_hdf5_write_$group_num$(file, num_write);
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_write_$group_num$(file, num);
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return trexio_json_write_$group_num$(file, num_write);
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,*/
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}
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@ -2219,6 +2242,12 @@ trexio_read_$group_num$_32 (trexio_t* const file, $group_num_dtype_single$* cons
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if (rc != TREXIO_SUCCESS) return rc;
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,*num = ($group_num_dtype_single$) num_64;
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/* Handle index type */
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if ($is_index$) {
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,*num += ($group_num_dtype_single$) 1;
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}
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return TREXIO_SUCCESS;
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}
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#+end_src
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@ -2232,20 +2261,26 @@ trexio_write_$group_num$_32 (trexio_t* const file, const $group_num_dtype_single
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//if (num <= 0) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
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if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
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/* Handle index type */
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$group_num_dtype_single$ num_write = num;
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if ($is_index$) {
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num_write -= ($group_num_dtype_single$) 1;
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}
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num);
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return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num_write);
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num);
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return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num_write);
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num);
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return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num_write);
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break;
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,*/
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}
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@ -17,6 +17,7 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
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// parameters to be written
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int num = 12;
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int nucl_index[12] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
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int state_id = 2;
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/*================= START OF TEST ==================*/
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@ -32,6 +33,10 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
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rc = trexio_write_basis_nucleus_index(file, nucl_index);
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assert (rc == TREXIO_SUCCESS);
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// write index attribute in a file
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rc = trexio_write_state_id(file, state_id);
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assert (rc == TREXIO_SUCCESS);
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// close current session
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rc = trexio_close(file);
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assert (rc == TREXIO_SUCCESS);
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@ -89,8 +94,9 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
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trexio_exit_code rc;
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// parameters to be read
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int num;
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int* nucl_index;
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int num = 0;
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int* nucl_index = NULL;
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int state_id = 0;
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/*================= START OF TEST ==================*/
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@ -103,6 +109,11 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
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assert (rc == TREXIO_SUCCESS);
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assert (num == 12);
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// read index attribute from the file
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rc = trexio_read_state_id(file, &state_id);
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assert (rc == TREXIO_SUCCESS);
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assert (state_id == 2);
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// read numerical dataset from the file
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nucl_index = (int*) calloc(num, sizeof(int));
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rc = trexio_read_basis_nucleus_index(file, nucl_index);
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@ -17,6 +17,7 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
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// parameters to be written
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int num = 12;
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int nucl_index[12] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
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int state_id = 2;
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/*================= START OF TEST ==================*/
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@ -32,6 +33,10 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
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rc = trexio_write_basis_nucleus_index(file, nucl_index);
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assert (rc == TREXIO_SUCCESS);
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// write index attribute in a file
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rc = trexio_write_state_id(file, state_id);
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assert (rc == TREXIO_SUCCESS);
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// close current session
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rc = trexio_close(file);
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assert (rc == TREXIO_SUCCESS);
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@ -89,8 +94,9 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
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trexio_exit_code rc;
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// parameters to be read
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int num;
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int* nucl_index;
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int num = 0;
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int* nucl_index = NULL;
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int state_id = 0;
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/*================= START OF TEST ==================*/
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@ -103,6 +109,11 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
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assert (rc == TREXIO_SUCCESS);
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assert (num == 12);
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// read index attribute from the file
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rc = trexio_read_state_id(file, &state_id);
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assert (rc == TREXIO_SUCCESS);
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assert (state_id == 2);
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// read numerical dataset from the file
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nucl_index = (int*) calloc(num, sizeof(int));
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rc = trexio_read_basis_nucleus_index(file, nucl_index);
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@ -85,6 +85,7 @@ subroutine test_write(file_name, back_end)
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integer :: i, j, n_buffers = 5
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integer(8) :: buf_size_sparse, buf_size_det, offset
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integer :: state_id
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buf_size_sparse = 100/n_buffers
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buf_size_det = 50/n_buffers
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@ -107,6 +108,7 @@ subroutine test_write(file_name, back_end)
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! parameters to be written
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nucleus_num = 12
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state_id = 2
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charge = (/ 6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1. /)
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coord = reshape( (/ 0.00000000d0, 1.39250319d0 , 0.00000000d0 , &
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-1.20594314d0, 0.69625160d0 , 0.00000000d0 , &
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@ -182,6 +184,9 @@ subroutine test_write(file_name, back_end)
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rc = trexio_write_basis_nucleus_index(trex_file, basis_nucleus_index)
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call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX')
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rc = trexio_write_state_id(trex_file, state_id)
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call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX TYPE')
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! write ao_num which will be used to determine the optimal size of int indices
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if (trexio_has_ao_num(trex_file) == TREXIO_HAS_NOT) then
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rc = trexio_write_ao_num(trex_file, ao_num)
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@ -302,6 +307,7 @@ subroutine test_read(file_name, back_end)
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integer*8 :: offset_det_data_read = 5
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integer*8 :: determinant_num
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integer :: int_num
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integer :: state_id
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! orbital lists
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integer*4 :: orb_list_up(150)
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@ -312,6 +318,7 @@ subroutine test_read(file_name, back_end)
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num = 12
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basis_shell_num = 24
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state_id = 0
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index_sparse_ao_2e_int_eri = 0
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value_sparse_ao_2e_int_eri = 0.0d0
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@ -379,6 +386,15 @@ subroutine test_read(file_name, back_end)
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call exit(-1)
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endif
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rc = trexio_read_state_id(trex_file, state_id)
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call trexio_assert(rc, TREXIO_SUCCESS)
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if (state_id == 2) then
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write(*,*) 'SUCCESS READ INDEX TYPE'
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else
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print *, 'FAILURE INDEX TYPE CHECK'
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call exit(-1)
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endif
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rc = trexio_read_nucleus_point_group(trex_file, sym_str, 10)
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call trexio_assert(rc, TREXIO_SUCCESS)
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@ -611,8 +611,13 @@ def get_detailed_num_dict (configuration: dict) -> dict:
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tmp_dict.update(get_dtype_dict(v2[0], 'num'))
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if v2[0] in ['int', 'dim', 'dim readonly']:
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tmp_dict['trex_json_int_type'] = v2[0]
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tmp_dict['is_index'] = 'false'
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elif v2[0] in ['index']:
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tmp_dict['trex_json_int_type'] = v2[0]
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tmp_dict['is_index'] = 'file->one_based'
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else:
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tmp_dict['trex_json_int_type'] = ''
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tmp_dict['is_index'] = 'false'
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num_dict[tmp_num] = tmp_dict
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26
trex.org
26
trex.org
@ -190,13 +190,14 @@
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The ~id~ and ~current_label~ attributes need to be specified for each file.
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#+NAME: state
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| Variable | Type | Dimensions | Description |
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|-----------------+-------+---------------+---------------------------------------------------------------------------------------------|
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| ~num~ | ~dim~ | | Number of states (including the ground state) |
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| ~id~ | ~int~ | | Index of the current state (0 is ground state) |
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| ~current_label~ | ~str~ | | Label of the current state |
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| ~label~ | ~str~ | ~(state.num)~ | Labels of all states |
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| ~file_name~ | ~str~ | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
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| Variable | Type | Dimensions | Description |
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|-----------------+---------+---------------+---------------------------------------------------------------------------------------------|
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| ~num~ | ~dim~ | | Number of states (including the ground state) |
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| ~id~ | ~index~ | | Index of the current state (0 is ground state) |
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| ~energy~ | ~float~ | | Energy of the current state |
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| ~current_label~ | ~str~ | | Label of the current state |
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| ~label~ | ~str~ | ~(state.num)~ | Labels of all states |
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| ~file_name~ | ~str~ | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
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#+CALL: json(data=state, title="state")
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@ -204,11 +205,12 @@
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:results:
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#+begin_src python :tangle trex.json
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"state": {
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"num" : [ "dim", [] ]
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, "id" : [ "int", [] ]
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, "current_label" : [ "str", [] ]
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, "label" : [ "str", [ "state.num" ] ]
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, "file_name" : [ "str", [ "state.num" ] ]
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"num" : [ "dim" , [] ]
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, "id" : [ "index", [] ]
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, "energy" : [ "float", [] ]
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, "current_label" : [ "str" , [] ]
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, "label" : [ "str" , [ "state.num" ] ]
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, "file_name" : [ "str" , [ "state.num" ] ]
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} ,
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#+end_src
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:end:
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