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41 KiB
41 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 |
qmckl_vector | Nuclear charges |
coord |
qmckl_matrix | Nuclear coordinates, in transposed format |
coord_date |
int64_t | Nuclear coordinates, date if modified |
rescale_factor_kappa |
double | The distance scaling factor |
Computed data:
nn_distance |
qmckl_matrix | Nucleus-nucleus distances |
nn_distance_date |
int64_t | Date when Nucleus-nucleus distances were computed |
nn_distance_rescaled |
qmckl_matrix | Nucleus-nucleus rescaled distances |
nn_distance_rescaled_date |
int64_t | Date when Nucleus-nucleus rescaled 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 nn_distance_rescaled_date;
int64_t coord_date;
qmckl_vector charge;
qmckl_matrix coord;
qmckl_matrix nn_distance;
qmckl_matrix nn_distance_rescaled;
double repulsion;
double rescale_factor_kappa;
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 */
ctx->nucleus.rescale_factor_kappa = 1.0;
return QMCKL_SUCCESS;
}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
#+NAME:pre2
#+NAME:post2
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.
qmckl_exit_code
qmckl_set_nucleus_rescale_factor(qmckl_context context,
const double kappa);Sets the rescale parameter for the nuclear distances.
Test
const double* nucl_charge = chbrclf_charge;
const double* nucl_coord = &(chbrclf_nucl_coord[0][0]);
const double nucl_rescale_factor_kappa = 2.0;
/* --- */
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);
assert(rc == QMCKL_SUCCESS);
assert(!qmckl_nucleus_provided(context));
rc = qmckl_get_nucleus_num (context, &n);
assert(rc == QMCKL_SUCCESS);
assert(n == chbrclf_nucl_num);
double k;
rc = qmckl_get_nucleus_rescale_factor (context, &k);
assert(rc == QMCKL_SUCCESS);
assert(k == 1.0);
rc = qmckl_set_nucleus_rescale_factor (context, nucl_rescale_factor_kappa);
assert(rc == QMCKL_SUCCESS);
rc = qmckl_get_nucleus_rescale_factor (context, &k);
assert(rc == QMCKL_SUCCESS);
assert(k == nucl_rescale_factor_kappa);
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);
assert(rc == QMCKL_SUCCESS);
assert(!qmckl_nucleus_provided(context));
rc = qmckl_get_nucleus_coord (context, 'N', nucl_coord2, 3*chbrclf_nucl_num);
assert(rc == QMCKL_SUCCESS);
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);
assert(rc == QMCKL_SUCCESS);
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);
assert(rc == QMCKL_SUCCESS);
rc = qmckl_get_nucleus_charge(context, nucl_charge2, chbrclf_nucl_num);
assert(rc == QMCKL_SUCCESS);
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_fTest
/* 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);Nucleus-nucleus rescaled distances
Get
qmckl_exit_code
qmckl_get_nucleus_nn_distance_rescaled(qmckl_context context,
double* distance_rescaled,
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_rescaled[nucl_num][nucl_num] | out | Nucleus-nucleus rescaled distances (au) |
integer function qmckl_compute_nn_distance_rescaled_f(context, nucl_num, rescale_factor_kappa, coord, nn_distance_rescaled) &
result(info)
use qmckl
implicit none
integer(qmckl_context), intent(in) :: context
integer*8 , intent(in) :: nucl_num
double precision , intent(in) :: rescale_factor_kappa
double precision , intent(in) :: coord(nucl_num,3)
double precision , intent(out) :: nn_distance_rescaled(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_rescaled(context, 'T', 'T', nucl_num, nucl_num, &
coord, nucl_num, &
coord, nucl_num, &
nn_distance_rescaled, nucl_num, rescale_factor_kappa)
end function qmckl_compute_nn_distance_rescaled_fTest
/* Reference input data */
/* TODO */
//assert(qmckl_nucleus_provided(context));
//
//double distance[nucl_num*nucl_num];
//rc = qmckl_get_nucleus_nn_distance(context, distance, nucl_num*nucl_num);
//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* 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_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);