qmckl/org/qmckl_trexio.org

#+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)

  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 = 0LL;

  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_prim_num_X",
                             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_prim_num_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_num);
      shell_prim_num = NULL;
      qmckl_free(context, tmp_array);
      tmp_array = NULL;
      return qmckl_failwith( context,
                             QMCKL_FAILURE,
                             "trexio_read_basis_shell_prim_num",
                             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);
        return qmckl_failwith( context,
                                QMCKL_FAILURE,
                                "trexio_read_basis_shell_prim_num",
                                "Irrelevant data in TREXIO file");
      }
      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);

    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