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#+TITLE: TREXIO I/O library
#+SETUPFILE: ../tools/theme.setup
#+INCLUDE: ../tools/lib.org
The [[https://trex-coe.github.io/trexio/trex.html][TREXIO library]] enables easy and efficient input/output of wave
function parameters. In this section we provide high-level functions
to prepare the context by reading the required data from a TREXIO file.
* Headers :noexport:
#+begin_src elisp :noexport :results none
(org-babel-lob-ingest "../tools/lib.org")
#+end_src
#+begin_src c :tangle (eval c_test) :noweb yes
#include "qmckl.h"
#include <assert.h>
#include <math.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "chbrclf.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
int main() {
qmckl_context context;
context = qmckl_context_create();
#ifdef HAVE_TREXIO
#+end_src
#+begin_src c :tangle (eval c)
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifdef HAVE_STDINT_H
#include <stdint.h>
#elif HAVE_INTTYPES_H
#include <inttypes.h>
#endif
#ifdef HAVE_TREXIO
#include <trexio.h>
#endif
#include <stdlib.h>
#include <string.h>
#include <stdbool.h>
#include <assert.h>
#include <math.h>
#include <stdio.h>
#include "qmckl.h"
#include "qmckl_memory_private_type.h"
#include "qmckl_memory_private_func.h"
#+end_src
* Local functions
Functions defined in this section are all local: they should not be
exposed in the API. To identify them, we append ~_X~ to
their name.
Users are not able to call directly these functions, so by
construction the context can't be ~NULL~, hence we can check this
with an ~assert~ statement.
In the functions defined in this section, we use as local variables
- ~rc~: the return code for QMCkl functions
- ~rcio~: the return code for TREXIO functions.
** Open file
We first define a helper function to open a file by first trying to
use the TEXT back end, and then the HDF5 back end. If both
strategies fail, a ~NULL~ pointer is returned. This will allow to
open only once the file and call multiple small functions to read
groups of data by passing the ~trexio_t~ handle.
#+begin_src c :tangle (eval c)
#ifdef HAVE_TREXIO
trexio_t* qmckl_trexio_open_X(const char* file_name, qmckl_exit_code* rc)
{
,*rc = QMCKL_SUCCESS;
trexio_t* file = NULL;
file = trexio_open(file_name, 'r', TREXIO_TEXT, rc);
if (file != NULL) return file;
file = trexio_open(file_name, 'r', TREXIO_HDF5, rc);
if (file != NULL) return file;
,*rc = QMCKL_FAILURE;
/* TODO
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_electron_up_num",
trexio_string_of_error(rcio));
*/
return NULL;
}
#endif
#+end_src
** Electron
In this section we read all the data into the electron data structure.
We read the number of up-spin and down-spin electrons.
#+begin_src c :tangle (eval c)
#ifdef HAVE_TREXIO
qmckl_exit_code
qmckl_trexio_read_electron_X(qmckl_context context, trexio_t* const file)
{
assert (context != (qmckl_context) 0);
assert (file != NULL);
int rcio = 0;
int64_t up_num = 0L;
int64_t dn_num = 0L;
rcio = trexio_read_electron_up_num_64(file, &up_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_electron_up_num",
trexio_string_of_error(rcio));
}
assert (up_num >= 0L);
rcio = trexio_read_electron_dn_num_64(file, &dn_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_electron_dn_num",
trexio_string_of_error(rcio));
}
assert (dn_num >= 0L);
qmckl_exit_code rc;
rc = qmckl_set_electron_num(context, up_num, dn_num);
return rc;
}
#endif
#+end_src
** Nucleus
In this section we read the number of nuclei, the molecular geometry and nuclear charges.
#+begin_src c :tangle (eval c)
#ifdef HAVE_TREXIO
qmckl_exit_code
qmckl_trexio_read_nucleus_X(qmckl_context context, trexio_t* const file)
{
assert (context != (qmckl_context) 0);
assert (file != NULL);
qmckl_exit_code rc;
int rcio = 0;
#+end_src
*** Number of nuclei
#+begin_src c :tangle (eval c)
int64_t nucleus_num = 0L;
rcio = trexio_read_nucleus_num_64(file, &nucleus_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_nucleus_num",
trexio_string_of_error(rcio));
}
assert (nucleus_num > 0);
rc = qmckl_set_nucleus_num(context, nucleus_num);
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** Nuclear charges
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
mem_info.size = nucleus_num * sizeof(double);
double* nucl_charge = (double*) qmckl_malloc(context, mem_info);
if (nucl_charge == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_nucleus_X",
NULL);
}
assert (nucl_charge != NULL);
rcio = trexio_read_safe_nucleus_charge_64(file, nucl_charge, nucleus_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_nucleus_charge",
trexio_string_of_error(rcio));
}
rc = qmckl_set_nucleus_charge(context, nucl_charge, nucleus_num);
qmckl_free(context, nucl_charge);
nucl_charge = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Nuclear coordinates
Now, we read the molecular geometry. It is stored in normal format
in the TREXIO file (~'N'~), so it will be automatically transposed internally.
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
mem_info.size = nucleus_num * 3 * sizeof(double);
double* nucl_coord = (double*) qmckl_malloc(context, mem_info);
if (nucl_coord == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_nucleus_X",
NULL);
}
assert (nucl_coord != NULL);
rcio = trexio_read_safe_nucleus_coord_64(file, nucl_coord, 3*nucleus_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_nucleus_charge",
trexio_string_of_error(rcio));
}
rc = qmckl_set_nucleus_coord(context, 'N', nucl_coord, 3*nucleus_num);
qmckl_free(context, nucl_coord);
nucl_coord = NULL;
if (rc != QMCKL_SUCCESS) {
return rc;
}
}
#+end_src
#+begin_src c :tangle (eval c)
assert ( qmckl_nucleus_provided(context) );
return QMCKL_SUCCESS;
}
#endif
#+end_src
** Basis set and AOs
In this section we read the atomic basis set and atomic orbitals.
#+begin_src c :tangle (eval c)
#ifdef HAVE_TREXIO
qmckl_exit_code
qmckl_trexio_read_ao_X(qmckl_context context, trexio_t* const file)
{
assert (context != (qmckl_context) 0);
assert (file != NULL);
qmckl_exit_code rc;
int rcio = 0;
int64_t nucleus_num = 0L;
rc = qmckl_get_nucleus_num(context, &nucleus_num);
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** Basis set type
#+begin_src c :tangle (eval c)
#define MAX_STR_LEN 1024
char basis_type[MAX_STR_LEN];
rcio = trexio_read_basis_type(file, basis_type, MAX_STR_LEN);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_type",
trexio_string_of_error(rcio));
}
if (basis_type[0] == 'G') {
rc = qmckl_set_ao_basis_type(context, basis_type[0]);
} else {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_type",
"Invalid basis type");
}
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** Number of shells
#+begin_src c :tangle (eval c)
int64_t shell_num = 0L;
rcio = trexio_read_basis_shell_num_64(file, &shell_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_shell_num",
trexio_string_of_error(rcio));
}
assert (shell_num > 0);
rc = qmckl_set_ao_basis_shell_num(context, shell_num);
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** Number of primitives
#+begin_src c :tangle (eval c)
int64_t prim_num = 0L;
rcio = trexio_read_basis_prim_num_64(file, &prim_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_prim_num",
trexio_string_of_error(rcio));
}
assert (prim_num > 0);
rc = qmckl_set_ao_basis_prim_num(context, prim_num);
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** Number of atomic orbitals
#+begin_src c :tangle (eval c)
int64_t ao_num = 0;
rcio = trexio_read_ao_num_64(file, &ao_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_ao_num",
trexio_string_of_error(rcio));
}
assert (ao_num > 0);
rc = qmckl_set_ao_basis_ao_num(context, ao_num);
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** Nucleus_index array
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = nucleus_num * sizeof(int64_t);
int64_t* nucleus_index = (int64_t*) qmckl_malloc(context, mem_info);
if (nucleus_index == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_nucleus_index_X",
NULL);
}
assert (nucleus_index != NULL);
/* Allocate temporary array */
mem_info.size = shell_num * sizeof(int64_t);
int64_t* tmp_array = (int64_t*) qmckl_malloc(context, mem_info);
if (tmp_array == NULL) {
qmckl_free(context, nucleus_index);
nucleus_index = NULL;
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_nucleus_index_X",
NULL);
}
assert (tmp_array != NULL);
/* Read in the temporary array */
rcio = trexio_read_safe_basis_nucleus_index_64(file, tmp_array, shell_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, tmp_array);
tmp_array = NULL;
qmckl_free(context, nucleus_index);
nucleus_index = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_nucleus_index",
trexio_string_of_error(rcio));
}
/* Reformat data */
for (int i=shell_num-1 ; i>=0 ; --i) {
const int k = tmp_array[i];
if (k < 0 || k >= nucleus_num) {
qmckl_free(context, tmp_array);
tmp_array = NULL;
qmckl_free(context, nucleus_index);
nucleus_index = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_nucleus_index",
"Irrelevant data in TREXIO file");
}
nucleus_index[k] = i;
}
qmckl_free(context, tmp_array);
tmp_array = NULL;
/* Store data */
rc = qmckl_set_ao_basis_nucleus_index(context, nucleus_index, shell_num);
qmckl_free(context, nucleus_index);
nucleus_index = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Number of shells per nucleus
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = nucleus_num * sizeof(int64_t);
int64_t* nucleus_shell_num = (int64_t*) qmckl_malloc(context, mem_info);
if (nucleus_shell_num == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_nucleus_shell_num_X",
NULL);
}
assert (nucleus_shell_num != NULL);
/* Allocate temporary array */
mem_info.size = shell_num * sizeof(int64_t);
int64_t* tmp_array = (int64_t*) qmckl_malloc(context, mem_info);
if (tmp_array == NULL) {
qmckl_free(context, nucleus_shell_num);
nucleus_shell_num = NULL;
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_nucleus_shell_num_X",
NULL);
}
assert (tmp_array != NULL);
/* Read in the temporary array */
rcio = trexio_read_safe_basis_nucleus_index_64(file, tmp_array, shell_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, tmp_array);
tmp_array = NULL;
qmckl_free(context, nucleus_shell_num);
nucleus_shell_num = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_nucleus_shell_num",
trexio_string_of_error(rcio));
}
/* Reformat data */
for (int i=0 ; i<nucleus_num ; ++i) {
nucleus_shell_num[i] = 0;
}
for (int i=0 ; i<shell_num ; ++i) {
const int k = tmp_array[i];
if (k < 0 || k >= nucleus_num) {
qmckl_free(context, tmp_array);
tmp_array = NULL;
qmckl_free(context, nucleus_shell_num);
nucleus_shell_num = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_nucleus_shell_num",
"Irrelevant data in TREXIO file");
}
nucleus_shell_num[k] += 1;
}
qmckl_free(context, tmp_array);
tmp_array = NULL;
/* Store data */
rc = qmckl_set_ao_basis_nucleus_shell_num(context, nucleus_shell_num, shell_num);
qmckl_free(context, nucleus_shell_num);
nucleus_shell_num = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Angular momentum
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = shell_num * sizeof(int32_t);
int32_t* shell_ang_mom = (int32_t*) qmckl_malloc(context, mem_info);
if (shell_ang_mom == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_shell_ang_mom_X",
NULL);
}
assert (shell_ang_mom != NULL);
/* Read data */
rcio = trexio_read_safe_basis_shell_ang_mom_32(file, shell_ang_mom, shell_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, shell_ang_mom);
shell_ang_mom = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_shell_ang_mom",
trexio_string_of_error(rcio));
}
/* Store data */
rc = qmckl_set_ao_basis_shell_ang_mom(context, shell_ang_mom, shell_num);
qmckl_free(context, shell_ang_mom);
shell_ang_mom = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Number of primitives per shell
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = shell_num * sizeof(int64_t);
int64_t* shell_prim_num = (int64_t*) qmckl_malloc(context, mem_info);
if (shell_prim_num == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_shell_index",
NULL);
}
assert (shell_prim_num != NULL);
/* Allocate temporary array */
mem_info.size = prim_num * sizeof(int64_t);
int64_t* tmp_array = (int64_t*) qmckl_malloc(context, mem_info);
if (tmp_array == NULL) {
qmckl_free(context, shell_prim_num);
shell_prim_num = NULL;
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_shell_index",
NULL);
}
assert (tmp_array != NULL);
/* Read data */
rcio = trexio_read_safe_basis_shell_index_64 (file, tmp_array, prim_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, shell_prim_num);
shell_prim_num = NULL;
qmckl_free(context, tmp_array);
tmp_array = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"qmckl_trexio_read_basis_shell_index",
trexio_string_of_error(rcio));
}
/* Reformat data */
for (int i=0 ; i<shell_num ; ++i) {
shell_prim_num[i] = 0;
}
for (int i=0 ; i<prim_num ; ++i) {
const int k = tmp_array[i];
if (k < 0 || k >= shell_num) {
qmckl_free(context, tmp_array);
qmckl_free(context, shell_prim_num);
char msg[128];
sprintf(&msg[0], "Irrelevant data in TREXIO file: k = %d", k);
return qmckl_failwith( context,
QMCKL_FAILURE,
"qmckl_trexio_read_basis_shell_index",
&msg[0]);
}
shell_prim_num[k] += 1;
}
qmckl_free(context, tmp_array);
tmp_array = NULL;
/* Store data */
rc = qmckl_set_ao_basis_shell_prim_num(context, shell_prim_num, shell_num);
qmckl_free(context, shell_prim_num);
shell_prim_num = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Indices of the primitives
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = shell_num * sizeof(int64_t);
int64_t* shell_prim_index = (int64_t*) qmckl_malloc(context, mem_info);
if (shell_prim_index == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_shell_prim_index_X",
NULL);
}
assert (shell_prim_index != NULL);
/* Allocate temporary array */
mem_info.size = prim_num * sizeof(int64_t);
int64_t* tmp_array = (int64_t*) qmckl_malloc(context, mem_info);
if (tmp_array == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_shell_prim_index_X",
NULL);
}
assert (tmp_array != NULL);
/* Read data */
rcio = trexio_read_safe_basis_shell_index_64(file, tmp_array, prim_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, shell_prim_index);
shell_prim_index = NULL;
qmckl_free(context, tmp_array);
tmp_array = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_shell_prim_index",
trexio_string_of_error(rcio));
}
/* Reformat data */
for (int i=prim_num-1 ; i>=0 ; --i) {
const int k = tmp_array[i];
if (k < 0 || k >= shell_num) {
qmckl_free(context, tmp_array);
tmp_array = NULL;
qmckl_free(context, shell_prim_index);
shell_prim_index = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_shell_prim_index",
"Irrelevant data in TREXIO file");
}
shell_prim_index[k] = i;
}
qmckl_free(context, tmp_array);
tmp_array = NULL;
/* Store data */
rc = qmckl_set_ao_basis_shell_prim_index(context, shell_prim_index, shell_num);
qmckl_free(context, shell_prim_index);
shell_prim_index = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Normalization of the shells
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = shell_num * sizeof(double);
double* shell_factor = (double*) qmckl_malloc(context, mem_info);
if (shell_factor == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_shell_factor_X",
NULL);
}
assert (shell_factor != NULL);
/* Read data */
rcio = trexio_read_safe_basis_shell_factor_64(file, shell_factor, shell_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, shell_factor);
shell_factor = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_shell_factor",
trexio_string_of_error(rcio));
}
/* Store data */
rc = qmckl_set_ao_basis_shell_factor(context, shell_factor, shell_num);
qmckl_free(context, shell_factor);
shell_factor = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Exponents
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = prim_num * sizeof(double);
double* exponent = (double*) qmckl_malloc(context, mem_info);
if (exponent == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_exponent_X",
NULL);
}
assert (exponent != NULL);
/* Read data */
rcio = trexio_read_safe_basis_exponent_64(file, exponent, prim_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, exponent);
exponent = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_exponent",
trexio_string_of_error(rcio));
}
/* Store data */
rc = qmckl_set_ao_basis_exponent(context, exponent, prim_num);
qmckl_free(context, exponent);
exponent = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Coefficients
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = prim_num * sizeof(double);
double* coefficient = (double*) qmckl_malloc(context, mem_info);
if (coefficient == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_coefficient_X",
NULL);
}
assert (coefficient != NULL);
/* Read data */
rcio = trexio_read_safe_basis_coefficient_64(file, coefficient, prim_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, coefficient);
coefficient = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_coefficient",
trexio_string_of_error(rcio));
}
/* Store data */
rc = qmckl_set_ao_basis_coefficient(context, coefficient, prim_num);
qmckl_free(context, coefficient);
coefficient = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** Normalization of the primitivies
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = prim_num * sizeof(double);
double* prim_factor = (double*) qmckl_malloc(context, mem_info);
if (prim_factor == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_basis_prim_factor_X",
NULL);
}
assert (prim_factor != NULL);
/* Read data */
rcio = trexio_read_safe_basis_prim_factor_64(file, prim_factor, prim_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, prim_factor);
prim_factor = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_basis_prim_factor",
trexio_string_of_error(rcio));
}
/* Read data */
rc = qmckl_set_ao_basis_prim_factor(context, prim_factor, prim_num);
qmckl_free(context, prim_factor);
prim_factor = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
*** AO Normalization
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
/* Allocate array for data */
mem_info.size = ao_num * sizeof(double);
double* ao_normalization = (double*) qmckl_malloc(context, mem_info);
if (ao_normalization == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_ao_normalization_X",
NULL);
}
assert (ao_normalization != NULL);
/* Read data */
rcio = trexio_read_safe_ao_normalization_64(file, ao_normalization, ao_num);
if (rcio != TREXIO_SUCCESS) {
qmckl_free(context, ao_normalization);
ao_normalization = NULL;
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_ao_normalization",
trexio_string_of_error(rcio));
}
/* Store data */
rc = qmckl_set_ao_basis_ao_factor(context, ao_normalization, ao_num);
qmckl_free(context, ao_normalization);
ao_normalization = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
#+begin_src c :tangle (eval c)
return QMCKL_SUCCESS;
}
#endif
#+end_src
** Molecular orbitals
In this section we read the MO coefficients.
#+begin_src c :tangle (eval c)
#ifdef HAVE_TREXIO
qmckl_exit_code
qmckl_trexio_read_mo_X(qmckl_context context, trexio_t* const file)
{
assert (context != (qmckl_context) 0);
assert (file != NULL);
qmckl_exit_code rc;
int rcio = 0;
int64_t ao_num = 0L;
rc = qmckl_get_ao_basis_ao_num(context, &ao_num);
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** Number of MOs
#+begin_src c :tangle (eval c)
int64_t mo_num = 0L;
rcio = trexio_read_mo_num_64(file, &mo_num);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_mo_num",
trexio_string_of_error(rcio));
}
assert (mo_num > 0);
rc = qmckl_set_mo_basis_mo_num(context, mo_num);
if (rc != QMCKL_SUCCESS)
return rc;
#+end_src
*** MO coefficients
#+begin_src c :tangle (eval c)
{
qmckl_memory_info_struct mem_info = qmckl_memory_info_struct_zero;
mem_info.size = ao_num * mo_num * sizeof(double);
double* mo_coef = (double*) qmckl_malloc(context, mem_info);
if (mo_coef == NULL) {
return qmckl_failwith( context,
QMCKL_ALLOCATION_FAILED,
"qmckl_trexio_read_mo_X",
NULL);
}
assert (mo_coef != NULL);
rcio = trexio_read_mo_coefficient_64(file, mo_coef);
if (rcio != TREXIO_SUCCESS) {
return qmckl_failwith( context,
QMCKL_FAILURE,
"trexio_read_mo_coefficient",
trexio_string_of_error(rcio));
}
rc = qmckl_set_mo_basis_coefficient(context, mo_coef, ao_num*mo_num);
qmckl_free(context, mo_coef);
mo_coef = NULL;
if (rc != QMCKL_SUCCESS)
return rc;
}
#+end_src
#+begin_src c :tangle (eval c)
return QMCKL_SUCCESS;
}
#endif
#+end_src
** TODO ECP
* Read everything
#+begin_src c :tangle (eval h_func)
qmckl_exit_code
qmckl_trexio_read(const qmckl_context context,
const char* file_name,
const int64_t size_max);
#+end_src
#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
interface
integer(c_int32_t) function qmckl_trexio_read &
(context, file_name, size_max) &
bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
integer (c_int64_t) , intent(in) , value :: context
integer (c_int64_t) , intent(in) , value :: size_max
character(c_char ) , intent(in) :: file_name(size_max)
end function qmckl_trexio_read
end interface
#+end_src
#+begin_src c :tangle (eval c)
qmckl_exit_code
qmckl_trexio_read(const qmckl_context context, const char* file_name, const int64_t size_max)
{
if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
return false;
}
qmckl_exit_code rc;
char file_name_new[size_max+1];
strncpy(file_name_new, file_name, size_max);
file_name_new[size_max] = '\0';
#ifdef HAVE_TREXIO
trexio_t* file = qmckl_trexio_open_X(file_name_new, &rc);
if (file == NULL) {
trexio_close(file);
return qmckl_failwith( context,
QMCKL_INVALID_ARG_2,
"qmckl_trexio_read",
trexio_string_of_error(rc));
}
assert (file != NULL);
rc = qmckl_trexio_read_electron_X(context, file);
if (rc != QMCKL_SUCCESS) {
trexio_close(file);
return rc;
}
rc = qmckl_trexio_read_nucleus_X(context, file);
if (rc != QMCKL_SUCCESS) {
trexio_close(file);
return rc;
}
rc = qmckl_trexio_read_ao_X(context, file);
if (rc != QMCKL_SUCCESS) {
trexio_close(file);
return rc;
}
rc = qmckl_trexio_read_mo_X(context, file);
if (rc != QMCKL_SUCCESS) {
trexio_close(file);
return rc;
}
trexio_close(file);
file = NULL;
#else
rc = qmckl_failwith( context,
QMCKL_FAILURE,
"qmckl_trexio_read",
"QMCkl was compiled without TREXIO");
#endif
return rc;
}
#+end_src
* Test
#+begin_src c :tangle (eval c_test)
#ifdef HAVE_TREXIO
qmckl_exit_code rc;
char filename[256];
#ifndef QMCKL_TEST_DIR
#error "QMCKL_TEST_DIR is not defined"
#endif
strncpy(filename, QMCKL_TEST_DIR,255);
strncat(filename, "/chbrclf", 255);
printf("Test file: %s\n", filename);
rc = qmckl_trexio_read(context, filename, 255);
qmckl_check(context, rc);
#+end_src
*** Electrons
#+begin_src c :tangle (eval c_test)
printf("Electrons\n");
int64_t up_num, dn_num;
rc = qmckl_get_electron_up_num(context, &up_num);
qmckl_check(context, rc);
assert (up_num == chbrclf_elec_up_num);
rc = qmckl_get_electron_down_num(context, &dn_num);
qmckl_check(context, rc);
assert (dn_num == chbrclf_elec_dn_num);
#+end_src
*** Nuclei
#+begin_src c :tangle (eval c_test)
printf("Nuclei\n");
int64_t nucl_num;
rc = qmckl_get_nucleus_num(context, &nucl_num);
qmckl_check(context, rc);
assert (nucl_num == chbrclf_nucl_num);
printf("Nuclear charges\n");
double * charge = (double*) malloc (nucl_num * sizeof(double));
rc = qmckl_get_nucleus_charge(context, charge, nucl_num);
qmckl_check(context, rc);
for (int i=0 ; i<nucl_num ; i++) {
assert (charge[i] == chbrclf_charge[i]);
}
free(charge);
charge = NULL;
printf("Nuclear coordinates\n");
double * coord = (double*) malloc (nucl_num * 3 * sizeof(double));
rc = qmckl_get_nucleus_coord(context, 'T', coord, 3*nucl_num);
qmckl_check(context, rc);
int k=0;
for (int j=0 ; j<3 ; ++j) {
for (int i=0 ; i<nucl_num ; ++i) {
// printf("%f %f\n", coord[k], chbrclf_nucl_coord[j][i]);
assert (coord[k] == chbrclf_nucl_coord[j][i]);
++k;
}
}
free(coord);
coord = NULL;
#+end_src
*** Atomic basis
#+begin_src c :tangle (eval c_test)
printf("Atomic basis\n");
char basis_type;
rc = qmckl_get_ao_basis_type(context, &basis_type);
assert (basis_type == 'G');
int64_t shell_num;
rc = qmckl_get_ao_basis_shell_num(context, &shell_num);
assert (shell_num == chbrclf_shell_num);
int64_t prim_num;
rc = qmckl_get_ao_basis_prim_num(context, &prim_num);
assert (prim_num == chbrclf_prim_num);
int64_t ao_num;
rc = qmckl_get_ao_basis_ao_num(context, &ao_num);
assert (ao_num == chbrclf_ao_num);
int64_t* nucleus_index = (int64_t*) malloc (nucl_num * sizeof(int64_t));
rc = qmckl_get_ao_basis_nucleus_index(context, nucleus_index, nucl_num);
qmckl_check(context, rc);
for (int i=0 ; i<nucl_num ; i++) {
assert (nucleus_index[i] == chbrclf_basis_nucleus_index[i]);
}
free(nucleus_index);
nucleus_index = NULL;
int64_t* nucleus_shell_num = (int64_t*) malloc (nucl_num * sizeof(int64_t));
rc = qmckl_get_ao_basis_nucleus_shell_num(context, nucleus_shell_num, nucl_num);
qmckl_check(context, rc);
for (int i=0 ; i<nucl_num ; i++) {
assert (nucleus_shell_num[i] == chbrclf_basis_nucleus_shell_num[i]);
}
free(nucleus_shell_num);
nucleus_shell_num = NULL;
int32_t* shell_ang_mom = (int32_t*) malloc (shell_num * sizeof(int32_t));
rc = qmckl_get_ao_basis_shell_ang_mom(context, shell_ang_mom, shell_num);
qmckl_check(context, rc);
for (int i=0 ; i<shell_num ; i++) {
assert (shell_ang_mom[i] == chbrclf_basis_shell_ang_mom[i]);
}
free(shell_ang_mom);
shell_ang_mom = NULL;
int64_t* shell_prim_num = (int64_t*) malloc (shell_num * sizeof(int64_t));
rc = qmckl_get_ao_basis_shell_prim_num(context, shell_prim_num, shell_num);
qmckl_check(context, rc);
for (int i=0 ; i<shell_num ; i++) {
assert (shell_prim_num[i] == chbrclf_basis_shell_prim_num[i]);
}
free(shell_prim_num);
shell_prim_num = NULL;
int64_t* shell_prim_index = (int64_t*) malloc (shell_num * sizeof(int64_t));
rc = qmckl_get_ao_basis_shell_prim_index(context, shell_prim_index, shell_num);
qmckl_check(context, rc);
for (int i=0 ; i<shell_num ; i++) {
assert (shell_prim_index[i] == chbrclf_basis_shell_prim_index[i]);
}
free(shell_prim_index);
shell_prim_index = NULL;
double* shell_factor = (double*) malloc (shell_num * sizeof(double));
rc = qmckl_get_ao_basis_shell_factor(context, shell_factor, shell_num);
qmckl_check(context, rc);
for (int i=0 ; i<shell_num ; i++) {
assert (fabs(shell_factor[i] - chbrclf_basis_shell_factor[i]) < 1.e-6);
}
free(shell_factor);
shell_factor = NULL;
double* exponent = (double*) malloc (prim_num * sizeof(double));
rc = qmckl_get_ao_basis_exponent(context, exponent, prim_num);
qmckl_check(context, rc);
for (int i=0 ; i<prim_num ; i++) {
assert (fabs((exponent[i] - chbrclf_basis_exponent[i])/chbrclf_basis_exponent[i]) < 1.e-7);
}
free(exponent);
exponent = NULL;
double* coefficient = (double*) malloc (prim_num * sizeof(double));
rc = qmckl_get_ao_basis_coefficient(context, coefficient, prim_num);
qmckl_check(context, rc);
for (int i=0 ; i<prim_num ; i++) {
assert (fabs((coefficient[i] - chbrclf_basis_coefficient[i])/chbrclf_basis_coefficient[i]) < 1.e-7);
}
free(coefficient);
coefficient = NULL;
double* prim_factor = (double*) malloc (prim_num * sizeof(double));
rc = qmckl_get_ao_basis_prim_factor(context, prim_factor, prim_num);
qmckl_check(context, rc);
for (int i=0 ; i<prim_num ; i++) {
assert (fabs((prim_factor[i] - chbrclf_basis_prim_factor[i])/chbrclf_basis_prim_factor[i]) < 1.e-7);
}
free(prim_factor);
prim_factor = NULL;
#endif
#+end_src
*** MO Basis
#+begin_src c :tangle (eval c_test)
printf("MOs\n");
int64_t mo_num;
rc = qmckl_get_mo_basis_mo_num(context, &mo_num);
qmckl_check(context, rc);
assert (mo_num == chbrclf_mo_num);
printf("MO coefs\n");
double * mo_coef = (double*) malloc (ao_num * mo_num * sizeof(double));
rc = qmckl_get_mo_basis_coefficient(context, mo_coef, mo_num*ao_num);
qmckl_check(context, rc);
for (int i=0 ; i<ao_num * mo_num ; i++) {
printf("%d %e %e %e\n", i, mo_coef[i], chbrclf_mo_coef[i],
( fabs(mo_coef[i] - chbrclf_mo_coef[i])/fabs(mo_coef[i])) );
assert ( fabs(mo_coef[i] - chbrclf_mo_coef[i])/fabs(mo_coef[i]) < 1.e-12 );
}
free(mo_coef);
charge = NULL;
#+end_src
* End of files :noexport:
*** Test
#+begin_src c :tangle (eval c_test)
if (qmckl_context_destroy(context) != QMCKL_SUCCESS)
return QMCKL_FAILURE;
#endif
return 0;
}
#+end_src
# -*- mode: org -*-
# vim: syntax=c
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