qmckl/org/qmckl_nucleus.org

Nucleus

• Context
  • Data structure
  • Access functions
  • Initialization functions
  • Test
• Computation
  • Nucleus-nucleus distances
    • Get
    • Compute
    • Test
  • Nuclear repulsion energy
    • Get
    • Compute
    • Test

All the data relative to the molecular geometry is described here.

Context

The following data stored in the context:

uninitialized	int32_t	Keeps bit set for uninitialized data
num	int64_t	Total number of nuclei
provided	bool	If true, nucleus is valid
charge	qmckl_vector	Nuclear charges
coord	qmckl_matrix	Nuclear coordinates, in transposed format
coord_date	int64_t	Nuclear coordinates, date if modified

Computed data:

nn_distance	qmckl_matrix	Nucleus-nucleus distances
nn_distance_date	int64_t	Date when Nucleus-nucleus distances were computed
repulsion	double	Nuclear repulsion energy
repulsion_date	int64_t	Date when the nuclear repulsion energy was computed

Data structure

typedef struct qmckl_nucleus_struct {
int64_t      num;
int64_t      repulsion_date;
int64_t      nn_distance_date;
int64_t      coord_date;
qmckl_vector charge;
qmckl_matrix coord;
qmckl_matrix nn_distance;
double       repulsion;
int32_t      uninitialized;
bool         provided;
} qmckl_nucleus_struct;

The uninitialized integer contains one bit set to one for each initialization function which has not been called. It becomes equal to zero after all initialization functions have been called. The struct is then initialized and provided == true. Some values are initialized by default, and are not concerned by this mechanism.

qmckl_exit_code qmckl_init_nucleus(qmckl_context context);

qmckl_exit_code qmckl_init_nucleus(qmckl_context context) {

if (qmckl_context_check(context) == QMCKL_NULL_CONTEXT) {
 return false;
}

qmckl_context_struct* const ctx = (qmckl_context_struct*) context;
assert (ctx != NULL);

ctx->nucleus.uninitialized = (1 << 3) - 1;

/* Default values */

return QMCKL_SUCCESS;
}

Access functions

When all the data relative to nuclei have been set, the following function returns true.

bool qmckl_nucleus_provided (const qmckl_context context);

Initialization functions

#+NAME:pre2

#+NAME:post

To set the data relative to the nuclei in the context, the following functions need to be called.

qmckl_exit_code
qmckl_set_nucleus_num(qmckl_context context,
                   const int64_t num);

Sets the number of nuclei.

qmckl_exit_code
qmckl_set_nucleus_charge(qmckl_context context,
                      const double* charge,
                      const int64_t size_max);

Sets the nuclear charges of all the atoms.

qmckl_exit_code
qmckl_set_nucleus_coord(qmckl_context context,
                     const char transp,
                     const double* coord,
                     const int64_t size_max);

Sets the nuclear coordinates of all the atoms. The coordinates are be given in atomic units.

Test

const double*   nucl_charge   = chbrclf_charge;
const double*   nucl_coord    = &(chbrclf_nucl_coord[0][0]);

/* --- */

qmckl_exit_code rc;

assert(!qmckl_nucleus_provided(context));

int64_t n;
rc = qmckl_get_nucleus_num (context, &n);
assert(rc == QMCKL_NOT_PROVIDED);


rc = qmckl_set_nucleus_num (context, chbrclf_nucl_num);
qmckl_check(context, rc);
assert(!qmckl_nucleus_provided(context));

rc = qmckl_get_nucleus_num (context, &n);
qmckl_check(context, rc);
assert(n == chbrclf_nucl_num);

double nucl_coord2[3*chbrclf_nucl_num];

rc = qmckl_get_nucleus_coord (context, 'T', nucl_coord2, 3*chbrclf_nucl_num);
assert(rc == QMCKL_NOT_PROVIDED);

rc = qmckl_set_nucleus_coord (context, 'T', &(nucl_coord[0]), 3*chbrclf_nucl_num);
qmckl_check(context, rc);

assert(!qmckl_nucleus_provided(context));

rc = qmckl_get_nucleus_coord (context, 'N', nucl_coord2, 3*chbrclf_nucl_num);
qmckl_check(context, rc);
for (size_t k=0 ; k<3 ; ++k) {
for (int64_t i=0 ; i<chbrclf_nucl_num ; ++i) {
assert( nucl_coord[chbrclf_nucl_num*k+i] == nucl_coord2[3*i+k] );
}
}

rc = qmckl_get_nucleus_coord (context, 'T', nucl_coord2, 3*chbrclf_nucl_num);
qmckl_check(context, rc);
for (int64_t i=0 ; i<3*chbrclf_nucl_num ; ++i) {
assert( nucl_coord[i] == nucl_coord2[i] );
}

double nucl_charge2[chbrclf_nucl_num];

rc = qmckl_get_nucleus_charge(context, nucl_charge2, chbrclf_nucl_num);
assert(rc == QMCKL_NOT_PROVIDED);

rc = qmckl_set_nucleus_charge(context, nucl_charge, chbrclf_nucl_num);
qmckl_check(context, rc);

rc = qmckl_get_nucleus_charge(context, nucl_charge2, chbrclf_nucl_num);
qmckl_check(context, rc);
for (int64_t i=0 ; i<chbrclf_nucl_num ; ++i) {
assert( nucl_charge[i] == nucl_charge2[i] );
}
assert(qmckl_nucleus_provided(context));

Computation

The computed data is stored in the context so that it can be reused by different kernels. To ensure that the data is valid, for each computed data the date of the context is stored when it is computed. To know if some data needs to be recomputed, we check if the date of the dependencies are more recent than the date of the data to compute. If it is the case, then the data is recomputed and the current date is stored.

Nucleus-nucleus distances

Get

qmckl_exit_code
qmckl_get_nucleus_nn_distance(qmckl_context context,
                          double* distance,
                          const int64_t size_max);

Compute

qmckl_context	context	in	Global state
int64_t	nucl_num	in	Number of nuclei
double	coord[3][nucl_num]	in	Nuclear coordinates (au)
double	nn_distance[nucl_num][nucl_num]	out	Nucleus-nucleus distances (au)

integer function qmckl_compute_nn_distance_f(context, nucl_num, coord, nn_distance) &
 result(info)
use qmckl
implicit none
integer(qmckl_context), intent(in)  :: context
integer*8             , intent(in)  :: nucl_num
double precision      , intent(in)  :: coord(nucl_num,3)
double precision      , intent(out) :: nn_distance(nucl_num,nucl_num)

integer*8 :: k

info = QMCKL_SUCCESS

if (context == QMCKL_NULL_CONTEXT) then
 info = QMCKL_INVALID_CONTEXT
 return
endif

if (nucl_num <= 0) then
 info = QMCKL_INVALID_ARG_2
 return
endif

info = qmckl_distance(context, 'T', 'T', nucl_num, nucl_num, &
      coord, nucl_num, &
      coord, nucl_num, &
      nn_distance, nucl_num)

end function qmckl_compute_nn_distance_f

Test

/* Reference input data */

assert(qmckl_nucleus_provided(context));

double distance[chbrclf_nucl_num*chbrclf_nucl_num];
rc = qmckl_get_nucleus_nn_distance(context, distance, chbrclf_nucl_num*chbrclf_nucl_num);
assert(distance[0] == 0.);
assert(distance[1] == distance[chbrclf_nucl_num]);
assert(fabs(distance[1]-2.070304721365169) < 1.e-12);

Nuclear repulsion energy

\[ V_{NN} = \sum_{A=1}^{N-1} \sum_{B>A}^N \frac{Q_A Q_B}{R_{AB}} \]

Get

qmckl_exit_code qmckl_get_nucleus_repulsion(qmckl_context context, double* const energy);

Compute

qmckl_context	context	in	Global state
int64_t	nucl_num	in	Number of nuclei
double	charge[nucl_num]	in	Nuclear charges (au)
double	nn_distance[nucl_num][nucl_num]	in	Nucleus-nucleus distances (au)
double	energy	out	Nuclear repulsion energy

integer function qmckl_compute_nucleus_repulsion_f(context, nucl_num, charge, nn_distance, energy) &
 result(info)
use qmckl
implicit none
integer(qmckl_context), intent(in)  :: context
integer*8             , intent(in)  :: nucl_num
double precision      , intent(in)  :: charge(nucl_num)
double precision      , intent(in)  :: nn_distance(nucl_num,nucl_num)
double precision      , intent(out) :: energy

integer*8 :: i, j

info = QMCKL_SUCCESS

if (context == QMCKL_NULL_CONTEXT) then
 info = QMCKL_INVALID_CONTEXT
 return
endif

if (nucl_num <= 0) then
 info = QMCKL_INVALID_ARG_2
 return
endif

energy = 0.d0
do j=2, nucl_num
 do i=1, j-1
    if (dabs(nn_distance(i,j)) > 1e-5) then
      energy = energy + charge(i) * charge(j) / nn_distance(i,j)
    endif
 end do
end do

end function qmckl_compute_nucleus_repulsion_f

Test

/* Reference input data */

assert(qmckl_nucleus_provided(context));

double rep;
rc = qmckl_get_nucleus_repulsion(context, &rep);
assert(rep - 318.2309879436158 < 1.e-10);