24 KiB
Nucleus
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 |
double[num] | Nuclear charges |
coord |
double[3][num] | Nuclear coordinates, in transposed format |
nn_distance |
double[num][num] | 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;
double* coord;
double* charge;
double* 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 bee called. It becomes equal
to zero after all initialization functions have been called. The
struct is then initialized and provided == true.
Access functions
#+NAME:post
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
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);
qmckl_exit_code qmckl_set_nucleus_charge (qmckl_context context, const double* charge);
qmckl_exit_code qmckl_set_nucleus_coord (qmckl_context context, const char transp, const double* coord);#+NAME:pre2
#+NAME:post2
To set the number of nuclei, use
The following function sets the nuclear charges of all the atoms.
The following function sets the nuclear coordinates of all the atoms. The coordinates should be given in atomic units.
Test
const int64_t nucl_num = chbrclf_nucl_num;
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, nucl_num);
assert(rc == QMCKL_SUCCESS);
assert(!qmckl_nucleus_provided(context));
rc = qmckl_get_nucleus_num (context, &n);
assert(rc == QMCKL_SUCCESS);
assert(n == nucl_num);
double nucl_coord2[3*nucl_num];
rc = qmckl_get_nucleus_coord (context, 'T', nucl_coord2);
assert(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_coord (context, 'T', &(nucl_coord[0]));
assert(rc == QMCKL_SUCCESS);
assert(!qmckl_nucleus_provided(context));
rc = qmckl_get_nucleus_coord (context, 'N', nucl_coord2);
assert(rc == QMCKL_SUCCESS);
for (size_t k=0 ; k<3 ; ++k) {
for (size_t i=0 ; i<nucl_num ; ++i) {
assert( nucl_coord[nucl_num*k+i] == nucl_coord2[3*i+k] );
}
}
rc = qmckl_get_nucleus_coord (context, 'T', nucl_coord2);
assert(rc == QMCKL_SUCCESS);
for (size_t i=0 ; i<3*nucl_num ; ++i) {
assert( nucl_coord[i] == nucl_coord2[i] );
}
double nucl_charge2[nucl_num];
rc = qmckl_get_nucleus_charge(context, nucl_charge2);
assert(rc == QMCKL_NOT_PROVIDED);
rc = qmckl_set_nucleus_charge(context, nucl_charge);
assert(rc == QMCKL_SUCCESS);
rc = qmckl_get_nucleus_charge(context, nucl_charge2);
assert(rc == QMCKL_SUCCESS);
for (size_t i=0 ; i<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);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_fTest
/* Reference input data */
assert(qmckl_nucleus_provided(context));
double distance[nucl_num*nucl_num];
rc = qmckl_get_nucleus_nn_distance(context, distance);
assert(distance[0] == 0.);
assert(distance[1] == distance[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* 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
energy = energy + charge(i) * charge(j) / nn_distance(i,j)
end do
end do
end function qmckl_compute_nucleus_repulsion_fTest
/* Reference input data */
assert(qmckl_nucleus_provided(context));
double rep;
rc = qmckl_get_nucleus_repulsion(context, &rep);
assert(rep - 318.2309879436158 < 1.e-10);