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Linear kernel #31

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Jul 13, 2017
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Linear kernel #31

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52568f1
Added linear kernel and test
andersx Jun 26, 2017
c79dde5
Updated documentation for kernels and removed compiler warning (from …
andersx Jun 26, 2017
6627122
Added global ARAD and linear global kernel
andersx Jul 4, 2017
ce010c0
Corrected ARAD global kernel to L2 distance
andersx Jul 13, 2017
202a526
Merge branch 'develop' into linear_kernel
andersx Jul 13, 2017
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89 changes: 63 additions & 26 deletions qml/farad_kernels.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -696,13 +696,14 @@ subroutine fget_global_symmetric_kernels_arad(q1, z1, n1, sigmas, nm1, nsigmas,
double precision, allocatable, dimension(:,:) :: atomic_distance

! Pre-computed terms in the full distance matrix
double precision, allocatable, dimension(:,:) :: selfl21
double precision, allocatable, dimension(:) :: selfl21

! Pre-computed sine terms
double precision, allocatable, dimension(:,:,:) :: sin1

! Value of PI at full FORTRAN precision.
double precision, parameter :: pi = 4.0d0 * atan(1.0d0)
double precision :: mol_dist

r_width2 = r_width**2
c_width2 = c_width**2
Expand All @@ -723,14 +724,22 @@ subroutine fget_global_symmetric_kernels_arad(q1, z1, n1, sigmas, nm1, nsigmas,
enddo
!$OMP END PARALLEL DO

allocate(selfl21(nm1, maxval(n1)))
allocate(selfl21(nm1))

!$OMP PARALLEL DO PRIVATE(ni)
selfl21 = 0.0d0

!$OMP PARALLEL DO PRIVATE(ni) REDUCTION(+:selfl21)
do i = 1, nm1
ni = n1(i)
do i_1 = 1, ni
selfl21(i,i_1) = atomic_distl2(q1(i,i_1,:,:), q1(i,i_1,:,:), n1(i), n1(i), &
& sin1(i,i_1,:), sin1(i,i_1,:), width, cut_distance, r_width, c_width)
do j_1 = 1, ni

selfl21(i) = selfl21(i) + atomic_distl2(q1(i,i_1,:,:), q1(i,j_1,:,:), n1(i), n1(i), &
& sin1(i,i_1,:), sin1(i,j_1,:), width, cut_distance, r_width, c_width) &
& * (r_width2/(r_width2 + (z1(i,i_1,1) - z1(i,j_1,1))**2) * &
& c_width2/(c_width2 + (z1(i,i_1,2) - z1(i,j_1,2))**2))

enddo
enddo
enddo
!$OMP END PARALLEL DO
Expand All @@ -740,10 +749,11 @@ subroutine fget_global_symmetric_kernels_arad(q1, z1, n1, sigmas, nm1, nsigmas,
kernels(:,:,:) = 0.0d0
atomic_distance(:,:) = 0.0d0

!$OMP PARALLEL DO PRIVATE(l2dist,atomic_distance,ni,nj) schedule(dynamic)
!$OMP PARALLEL DO PRIVATE(l2dist,atomic_distance,ni,nj,mol_dist) schedule(dynamic)
do j = 1, nm1
nj = n1(j)
do i = 1, j
do i = 1, j! nm1

ni = n1(i)

atomic_distance(:,:) = 0.0d0
Expand All @@ -754,17 +764,18 @@ subroutine fget_global_symmetric_kernels_arad(q1, z1, n1, sigmas, nm1, nsigmas,
l2dist = atomic_distl2(q1(i,i_1,:,:), q1(j,j_1,:,:), n1(i), n1(j), &
& sin1(i,i_1,:), sin1(j,j_1,:), width, cut_distance, r_width, c_width)

l2dist = selfl21(i,i_1) + selfl21(j,j_1) - 2.0d0 * l2dist &
& * (r_width2/(r_width2 + (z1(i,i_1,1) - z1(j,j_1,1))**2) &
& * c_width2/(c_width2 + (z1(i,i_1,2) - z1(j,j_1,2))**2))
L2dist = l2dist * (r_width2/(r_width2 + (z1(i,i_1,1) - z1(j,j_1,1))**2) * &
& c_width2/(c_width2 + (z1(i,i_1,2) - z1(j,j_1,2))**2))

atomic_distance(i_1,j_1) = l2dist

enddo
enddo

mol_dist = selfl21(i) + selfl21(j) - 2.0d0 * sum(atomic_distance(:ni,:nj))

do k = 1, nsigmas
kernels(k, i, j) = exp(sum(atomic_distance(:ni,:nj)) * inv_sigma2(k))
kernels(k, i, j) = exp(mol_dist * inv_sigma2(k))
kernels(k, j, i) = kernels(k, i, j)
enddo

Expand Down Expand Up @@ -834,8 +845,8 @@ subroutine fget_global_kernels_arad(q1, q2, z1, z2, n1, n2, sigmas, nm1, nm2, ns
double precision, allocatable, dimension(:,:) :: atomic_distance

! Pre-computed terms in the full distance matrix
double precision, allocatable, dimension(:,:) :: selfl21
double precision, allocatable, dimension(:,:) :: selfl22
double precision, allocatable, dimension(:) :: selfl21
double precision, allocatable, dimension(:) :: selfl22

! Pre-computed sine terms
double precision, allocatable, dimension(:,:,:) :: sin1
Expand All @@ -844,6 +855,8 @@ subroutine fget_global_kernels_arad(q1, q2, z1, z2, n1, n2, sigmas, nm1, nm2, ns
! Value of PI at full FORTRAN precision.
double precision, parameter :: pi = 4.0d0 * atan(1.0d0)

double precision :: mol_dist

r_width2 = r_width**2
c_width2 = c_width**2

Expand Down Expand Up @@ -882,25 +895,43 @@ subroutine fget_global_kernels_arad(q1, q2, z1, z2, n1, n2, sigmas, nm1, nm2, ns
enddo
!$OMP END PARALLEL DO

allocate(selfl21(nm1, maxval(n1)))
allocate(selfl22(nm2, maxval(n2)))
allocate(selfl21(nm1))
allocate(selfl22(nm2))

!$OMP PARALLEL DO PRIVATE(ni)
selfl21 = 0.0d0
selfl22 = 0.0d0

!$OMP PARALLEL DO PRIVATE(ni) REDUCTION(+:selfl21)
do i = 1, nm1
ni = n1(i)
do i_1 = 1, ni
selfl21(i,i_1) = atomic_distl2(q1(i,i_1,:,:), q1(i,i_1,:,:), n1(i), n1(i), &
& sin1(i,i_1,:), sin1(i,i_1,:), width, cut_distance, r_width, c_width)
do j_1 = 1, ni

selfl21(i) = selfl21(i) + atomic_distl2(q1(i,i_1,:,:), q1(i,j_1,:,:), n1(i), n1(i), &
& sin1(i,i_1,:), sin1(i,j_1,:), width, cut_distance, r_width, c_width) &
& * (r_width2/(r_width2 + (z1(i,i_1,1) - z1(i,j_1,1))**2) * &
& c_width2/(c_width2 + (z1(i,i_1,2) - z1(i,j_1,2))**2))

enddo

enddo
enddo
!$OMP END PARALLEL DO

!$OMP PARALLEL DO PRIVATE(ni)
!$OMP PARALLEL DO PRIVATE(ni) REDUCTION(+:selfl22)
do i = 1, nm2
ni = n2(i)
do i_1 = 1, ni
selfl22(i,i_1) = atomic_distl2(q2(i,i_1,:,:), q2(i,i_1,:,:), n2(i), n2(i), &
& sin2(i,i_1,:), sin2(i,i_1,:), width, cut_distance, r_width, c_width)
do j_1 = 1, ni

selfl22(i) = selfl22(i) + atomic_distl2(q2(i,i_1,:,:), q2(i,j_1,:,:), n2(i), n2(i), &
& sin2(i,i_1,:), sin2(i,j_1,:), width, cut_distance, r_width, c_width) &
&* (r_width2/(r_width2 + (z2(i,i_1,1) - z2(i,j_1,1))**2) * &
& c_width2/(c_width2 + (z2(i,i_1,2) - z2(i,j_1,2))**2))


enddo

enddo
enddo
!$OMP END PARALLEL DO
Expand All @@ -911,7 +942,9 @@ subroutine fget_global_kernels_arad(q1, q2, z1, z2, n1, n2, sigmas, nm1, nm2, ns
kernels(:,:,:) = 0.0d0
atomic_distance(:,:) = 0.0d0

!$OMP PARALLEL DO PRIVATE(l2dist,atomic_distance,ni,nj) schedule(dynamic)

!$OMP PARALLEL DO PRIVATE(l2dist,atomic_distance,ni,nj,mol_dist) schedule(dynamic)

do j = 1, nm2
nj = n2(j)
do i = 1, nm1
Expand All @@ -925,17 +958,21 @@ subroutine fget_global_kernels_arad(q1, q2, z1, z2, n1, n2, sigmas, nm1, nm2, ns
l2dist = atomic_distl2(q1(i,i_1,:,:), q2(j,j_1,:,:), n1(i), n2(j), &
& sin1(i,i_1,:), sin2(j,j_1,:), width, cut_distance, r_width, c_width)

l2dist = selfl21(i,i_1) + selfl22(j,j_1) - 2.0d0 * l2dist &
& * (r_width2/(r_width2 + (z1(i,i_1,1) - z2(j,j_1,1))**2) * &
& c_width2/(c_width2 + (z1(i,i_1,2) - z2(j,j_1,2))**2))

L2dist = l2dist * (r_width2/(r_width2 + (z1(i,i_1,1) - z2(j,j_1,1))**2) * &
& c_width2/(c_width2 + (z1(i,i_1,2) - z2(j,j_1,2))**2))


atomic_distance(i_1,j_1) = l2dist

enddo
enddo

mol_dist = selfl21(i) + selfl22(j) - 2.0d0 * sum(atomic_distance(:ni,:nj))

do k = 1, nsigmas
kernels(k, i, j) = exp(sum(atomic_distance(:ni,:nj)) * inv_sigma2(k))
kernels(k, i, j) = exp(mol_dist * inv_sigma2(k))

enddo

enddo
Expand Down