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descriptors_noncommercial.inc
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! HND XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
! HND X
! HND X GAP (Gaussian Approximation Potental)
! HND X
! HND X
! HND X Portions of GAP were written by Albert Bartok-Partay, Gabor Csanyi,
! HND X Copyright 2006-2021.
! HND X
! HND X Portions of GAP were written by Noam Bernstein as part of
! HND X his employment for the U.S. Government, and are not subject
! HND X to copyright in the USA.
! HND X
! HND X GAP is published and distributed under the
! HND X Academic Software License v1.0 (ASL)
! HND X
! HND X GAP is distributed in the hope that it will be useful for non-commercial
! HND X academic research, but WITHOUT ANY WARRANTY; without even the implied
! HND X warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
! HND X ASL for more details.
! HND X
! HND X You should have received a copy of the ASL along with this program
! HND X (e.g. in a LICENSE.md file); if not, you can write to the original licensors,
! HND X Gabor Csanyi or Albert Bartok-Partay. The ASL is also published at
! HND X http://github.com/gabor1/ASL
! HND X
! HND X When using this software, please cite the following reference:
! HND X
! HND X A. P. Bartok et al Physical Review Letters vol 104 p136403 (2010)
! HND X
! HND X When using the SOAP kernel or its variants, please additionally cite:
! HND X
! HND X A. P. Bartok et al Physical Review B vol 87 p184115 (2013)
! HND X
! HND XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
! HND X
! HND X
! HND X This file contains descriptors written by others, not A. P. Bartok and Gabor Csanyi
! HND X and the code here is owned by their respective authors, as indicated below.
! HND X
!!!!!!!!
!!! Work of Wojciech Szlachta BEGINS here
!!!!!!!!
subroutine bond_real_space_initialise(this,args_str,error)
type(bond_real_space), intent(inout) :: this
character(len=*), intent(in) :: args_str
integer, optional, intent(out) :: error
type(Dictionary) :: params
INIT_ERROR(error)
call finalise(this)
call initialise(params)
call param_register(params, 'bond_cutoff', '0.00', this%bond_cutoff, help_string="Bond cutoff for bond_real_space-type descriptors")
call param_register(params, 'bond_transition_width', '0.00', this%bond_transition_width, help_string="Bond transition width for bond_real_space-type descriptors")
call param_register(params, 'cutoff', '0.00', this%cutoff, help_string="Space cutoff for bond_real_space-type descriptors")
call param_register(params, 'transition_width', '0.00', this%transition_width, help_string="Space transition width for bond_real_space-type descriptors")
call param_register(params, 'atom_gaussian_width', '0.00', this%atom_sigma, help_string="Atom sigma for bond_real_space-type descriptors", altkey='atom_sigma')
call param_register(params, 'max_neighbours', '0', this%max_neighbours, help_string="Maximum number of neighbours")
if (.not. param_read_line(params, args_str, ignore_unknown=.true.,task='bond_real_space_initialise args_str')) then
RAISE_ERROR("bond_real_space_initialise failed to parse args_str='"//trim(args_str)//"'", error)
endif
call finalise(params)
this%initialised = .true.
endsubroutine bond_real_space_initialise
subroutine bond_real_space_finalise(this,error)
type(bond_real_space), intent(inout) :: this
integer, optional, intent(out) :: error
INIT_ERROR(error)
if(.not. this%initialised) return
this%bond_cutoff = 0.0_dp
this%bond_transition_width = 0.0_dp
this%cutoff = 0.0_dp
this%transition_width = 0.0_dp
this%atom_sigma = 0.0_dp
this%max_neighbours = 0
this%initialised = .false.
endsubroutine bond_real_space_finalise
subroutine bond_real_space_calc(this,at,descriptor_out,do_descriptor,do_grad_descriptor,args_str,error)
type(bond_real_space), intent(in) :: this
type(atoms), intent(in) :: at
type(descriptor_data), intent(out) :: descriptor_out
logical, intent(in), optional :: do_descriptor, do_grad_descriptor
character(len=*), intent(in), optional :: args_str
integer, optional, intent(out) :: error
type(Dictionary) :: params
character(STRING_LENGTH) :: atom_mask_name
logical :: has_atom_mask_name
logical, dimension(:), pointer :: atom_mask_pointer
type(atoms) :: at_copy
logical :: my_do_descriptor, my_do_grad_descriptor
integer :: n_descriptors, n_cross, i_desc, i, j, n, k, m, m_index, l, &
ij_neighbours, n_index
integer, dimension(3) :: shift_j, shift_k
real(dp) :: r_ij, r_ijk
real(dp) :: atom_i(3), atom_j(3), atom_k(3), bond(3), bond_len
real(dp) :: atom_i_cross_atom_j(3), atom_i_normsq_min_atom_j_normsq
real(dp), allocatable :: r(:,:), z(:), c(:)
real(dp) :: self_overlap
real(dp), allocatable :: dr(:,:,:,:), dz(:,:,:), dc(:,:,:)
real(dp), allocatable :: dself_overlap(:,:)
integer, allocatable :: ii(:)
real(dp), allocatable :: pos(:,:)
real(dp) :: r_m_cross_r_l(3)
INIT_ERROR(error)
call system_timer('bond_real_space_calc')
if(.not. this%initialised) then
RAISE_ERROR("bond_real_space_calc: descriptor object not initialised", error)
endif
my_do_descriptor = optional_default(.false., do_descriptor)
my_do_grad_descriptor = optional_default(.false., do_grad_descriptor)
if( .not. my_do_descriptor .and. .not. my_do_grad_descriptor ) return
call finalise(descriptor_out)
atom_mask_pointer => null()
if(present(args_str)) then
call initialise(params)
call param_register(params, 'atom_mask_name', 'NONE', atom_mask_name, has_value_target=has_atom_mask_name, &
help_string="Name of a logical property in the atoms object. For atoms where this property is true descriptors are " // &
"calculated.")
if (.not. param_read_line(params,args_str,ignore_unknown=.true.,task='bond_real_space_calc args_str')) then
RAISE_ERROR("bond_real_space_calc failed to parse args_str='"//trim(args_str)//"'", error)
endif
call finalise(params)
if( has_atom_mask_name ) then
if (.not. assign_pointer(at, trim(atom_mask_name), atom_mask_pointer)) then
RAISE_ERROR("bond_real_space_calc did not find "//trim(atom_mask_name)//" property in the atoms object.", error)
endif
RAISE_ERROR("bond_real_space_calc cannot use atom masks yet.",error)
else
atom_mask_pointer => null()
endif
endif
call descriptor_sizes(this,at,n_descriptors,n_cross,n_index=n_index,error=error)
allocate(descriptor_out%x(n_descriptors))
i_desc = 0
do i = 1, at%N
do n = 1, n_neighbours(at, i)
j = neighbour(at, i, n, shift=shift_j, distance=r_ij, max_dist=this%bond_cutoff)
if(j == 0) cycle
i_desc = i_desc + 1
atom_i = at%pos(:,i)
atom_j = at%pos(:,j) + matmul(at%lattice, shift_j)
at_copy = at
call add_atoms(at_copy, 0.5_dp * (atom_i + atom_j), 1)
call calc_connect(at_copy)
ij_neighbours = 0
do m = 1, n_neighbours(at_copy, at%N + 1)
k = neighbour(at_copy, at%N + 1, m, max_dist=this%cutoff)
if(k == 0) cycle
if(at_copy%pos(:,k) .feq. at_copy%pos(:,at%N + 1)) cycle
ij_neighbours = ij_neighbours + 1
enddo
if(ij_neighbours > this%max_neighbours) then
RAISE_ERROR("bond_real_space_calc: number of neighbours exceeds max_neighbours", error)
endif
if(my_do_descriptor .or. my_do_grad_descriptor) then
allocate(r(3,ij_neighbours), z(ij_neighbours), c(ij_neighbours))
allocate(ii(ij_neighbours), pos(3,ij_neighbours))
r = 0.0_dp
z = 0.0_dp
c = 0.0_dp
self_overlap = 0.0_dp
bond = atom_i - atom_j
bond_len = norm(bond)
atom_i_cross_atom_j = atom_i .cross. atom_j
atom_i_normsq_min_atom_j_normsq = normsq(atom_i) - normsq(atom_j)
ii = 0
pos = 0.0_dp
if(my_do_grad_descriptor) then
allocate(dr(3,ij_neighbours,3,ij_neighbours), dz(ij_neighbours,3,ij_neighbours), dc(ij_neighbours,3,ij_neighbours), dself_overlap(3,ij_neighbours))
dr = 0.0_dp
dz = 0.0_dp
dc = 0.0_dp
dself_overlap = 0.0_dp
endif
m_index = 2
do m = 1, n_neighbours(at_copy, at%N + 1)
k = neighbour(at_copy, at%N + 1, m, shift=shift_k, distance=r_ijk, max_dist=this%cutoff)
if(k == 0) cycle
if(at_copy%pos(:,k) .feq. at_copy%pos(:,at%N + 1)) cycle
atom_k = at_copy%pos(:,k) + matmul(at_copy%lattice, shift_k)
if(atom_k .feq. atom_i) then
! r remains zero
z(1) = 0.5_dp * bond_len
c(1) = coordination_function(r_ijk, this%cutoff, this%transition_width)
ii(1) = k
pos(:,1) = atom_k
if(my_do_grad_descriptor) then
! dr remains zero
dz(1,:,1) = 0.5_dp * bond / bond_len
dz(1,:,2) = - dz(1,:,1)
dc(1,:,1) = 0.25_dp * dcoordination_function(r_ijk, this%cutoff, this%transition_width) * bond / r_ijk
dc(1,:,2) = - dc(1,:,1)
endif
elseif(atom_k .feq. atom_j) then
! r remain zero
z(2) = -0.5_dp * bond_len
c(2) = coordination_function(r_ijk, this%cutoff, this%transition_width)
ii(2) = k
pos(:,2) = atom_k
if(my_do_grad_descriptor) then
! dr remains zero
dz(2,:,1) = -0.5_dp * bond / bond_len
dz(2,:,2) = - dz(2,:,1)
dc(2,:,1) = -0.25_dp * dcoordination_function(r_ijk, this%cutoff, this%transition_width) * bond / r_ijk
dc(2,:,2) = - dc(2,:,1)
endif
else
m_index = m_index + 1
r(:,m_index) = ((atom_k .cross. bond) + atom_i_cross_atom_j) / bond_len
z(m_index) = ((atom_k .dot. bond) - 0.5_dp * atom_i_normsq_min_atom_j_normsq) / bond_len
c(m_index) = coordination_function(r_ijk, this%cutoff, this%transition_width)
ii(m_index) = k
pos(:,m_index) = atom_k
if(my_do_grad_descriptor) then
dr(:,m_index,1,1) = ((/ 0.0_dp, atom_k(3) - atom_j(3), atom_j(2) - atom_k(2) /) / bond_len) - (r(:,m_index) * bond(1) / bond_len**2)
dr(:,m_index,2,1) = ((/ atom_j(3) - atom_k(3), 0.0_dp, atom_k(1) - atom_j(1) /) / bond_len) - (r(:,m_index) * bond(2) / bond_len**2)
dr(:,m_index,3,1) = ((/ atom_k(2) - atom_j(2), atom_j(1) - atom_k(1), 0.0_dp /) / bond_len) - (r(:,m_index) * bond(3) / bond_len**2)
dz(m_index,:,1) = ((atom_k - atom_i) / bond_len) - (z(m_index) * bond / bond_len**2)
dc(m_index,:,1) = -0.5_dp * dcoordination_function(r_ijk, this%cutoff, this%transition_width) * (atom_k - at_copy%pos(:,at%N + 1)) / r_ijk
dr(:,m_index,1,2) = - dr(:,m_index,1,1) + ((/ 0.0_dp, bond(3), - bond(2) /) / bond_len)
dr(:,m_index,2,2) = - dr(:,m_index,2,1) + ((/ - bond(3), 0.0_dp, bond(1) /) / bond_len)
dr(:,m_index,3,2) = - dr(:,m_index,3,1) + ((/ bond(2), - bond(1), 0.0_dp /) / bond_len)
dz(m_index,:,2) = - dz(m_index,:,1) - (bond / bond_len)
dc(m_index,:,2) = dc(m_index,:,1)
dr(:,m_index,1,m_index) = (/ 0.0_dp, - bond(3), bond(2) /) / bond_len
dr(:,m_index,2,m_index) = (/ bond(3), 0.0_dp, - bond(1) /) / bond_len
dr(:,m_index,3,m_index) = (/ - bond(2), bond(1), 0.0_dp /) / bond_len
dz(m_index,:,m_index) = bond / bond_len
dc(m_index,:,m_index) = -2.0_dp * dc(m_index,:,1)
endif
endif
enddo
endif
if(my_do_descriptor) then
allocate(descriptor_out%x(i_desc)%data(2 + (1 + 2 * this%max_neighbours) * this%max_neighbours))
allocate(descriptor_out%x(i_desc)%ci(n_index))
descriptor_out%x(i_desc)%data = 0.0_dp
do m = 1, ij_neighbours
self_overlap = self_overlap + c(m)**2
if(m == 1) then
descriptor_out%x(i_desc)%data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * m)) = z(m)
elseif(m == 2) then
descriptor_out%x(i_desc)%data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * m)) = z(m)
self_overlap = self_overlap + 2.0_dp * c(m) * c(m - 1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2 )
else
do l = 3, ij_neighbours
if(l == m) then
descriptor_out%x(i_desc)%data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1) = normsq(r(:,m))
descriptor_out%x(i_desc)%data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l)) = z(m)
else
descriptor_out%x(i_desc)%data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1) = r(:,m) .dot. r(:,l)
descriptor_out%x(i_desc)%data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l)) = ((r(:,m) .cross. r(:,l)) .dot. bond) / bond_len
endif
if(l < m) then
self_overlap = self_overlap + 2.0_dp * c(m) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 )
endif
enddo
endif
enddo
descriptor_out%x(i_desc)%data(1) = real(ij_neighbours, dp)
descriptor_out%x(i_desc)%data(2) = self_overlap
descriptor_out%x(i_desc)%data(3:ij_neighbours + 2) = c
descriptor_out%x(i_desc)%covariance_cutoff = coordination_function(r_ij, this%bond_cutoff, this%bond_transition_width)
descriptor_out%x(i_desc)%ci(:) = (/ i, j /)
descriptor_out%x(i_desc)%has_data = .true.
endif
if(my_do_grad_descriptor) then
allocate(descriptor_out%x(i_desc)%grad_data(2 + (1 + 2 * ij_neighbours) * ij_neighbours,3,ij_neighbours))
allocate(descriptor_out%x(i_desc)%ii(ij_neighbours))
allocate(descriptor_out%x(i_desc)%pos(3,ij_neighbours))
allocate(descriptor_out%x(i_desc)%grad_covariance_cutoff(3,ij_neighbours))
allocate(descriptor_out%x(i_desc)%has_grad_data(ij_neighbours))
descriptor_out%x(i_desc)%grad_data = 0.0_dp
do m = 1, ij_neighbours
dself_overlap(:,1) = dself_overlap(:,1) + 2.0_dp * c(m) * dc(m,:,1)
dself_overlap(:,2) = dself_overlap(:,2) + 2.0_dp * c(m) * dc(m,:,2)
if(m == 1) then
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * m),:,1) = dz(m,:,1)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * m),:,2) = dz(m,:,2)
elseif(m == 2) then
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * m),:,1) = dz(m,:,1)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * m),:,2) = dz(m,:,2)
dself_overlap(:,1) = dself_overlap(:,1) + 2.0_dp * dc(m,:,1) * c(m - 1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(m - 1,:,1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2 ) \
+ c(m) * c(m - 1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2 ) \
* (pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2
dself_overlap(:,2) = dself_overlap(:,2) + 2.0_dp * dc(m,:,2) * c(m - 1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(m - 1,:,2) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2 ) \
+ c(m) * c(m - 1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,m - 1)) / this%atom_sigma**2 ) \
* (pos(:,m - 1) - pos(:,m)) / this%atom_sigma**2
else
dself_overlap(:,m) = dself_overlap(:,m) + 2.0_dp * c(m) * dc(m,:,m)
do l = 3, ij_neighbours
if(l == m) then
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,1,1) = 2.0_dp * (r(:,m) .dot. dr(:,m,1,1))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,2,1) = 2.0_dp * (r(:,m) .dot. dr(:,m,2,1))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,3,1) = 2.0_dp * (r(:,m) .dot. dr(:,m,3,1))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),:,1) = dz(m,:,1)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,1,2) = 2.0_dp * (r(:,m) .dot. dr(:,m,1,2))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,2,2) = 2.0_dp * (r(:,m) .dot. dr(:,m,2,2))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,3,2) = 2.0_dp * (r(:,m) .dot. dr(:,m,3,2))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),:,2) = dz(m,:,2)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,1,m) = 2.0_dp * (r(:,m) .dot. dr(:,m,1,m))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,2,m) = 2.0_dp * (r(:,m) .dot. dr(:,m,2,m))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,3,m) = 2.0_dp * (r(:,m) .dot. dr(:,m,3,m))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),:,m) = dz(m,:,m)
else
r_m_cross_r_l = r(:,m) .cross. r(:,l)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,1,1) = (dr(:,m,1,1) .dot. r(:,l)) + (r(:,m) .dot. dr(:,l,1,1))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,2,1) = (dr(:,m,2,1) .dot. r(:,l)) + (r(:,m) .dot. dr(:,l,2,1))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,3,1) = (dr(:,m,3,1) .dot. r(:,l)) + (r(:,m) .dot. dr(:,l,3,1))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),1,1) = ((((dr(:,m,1,1) .cross. r(:,l)) + (r(:,m) .cross. dr(:,l,1,1))) .dot. bond) + (r_m_cross_r_l .dot. ((/ 1.0_dp, 0.0_dp, 0.0_dp /) - (bond * bond(1) / bond_len**2)))) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),2,1) = ((((dr(:,m,2,1) .cross. r(:,l)) + (r(:,m) .cross. dr(:,l,2,1))) .dot. bond) + (r_m_cross_r_l .dot. ((/ 0.0_dp, 1.0_dp, 0.0_dp /) - (bond * bond(2) / bond_len**2)))) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),3,1) = ((((dr(:,m,3,1) .cross. r(:,l)) + (r(:,m) .cross. dr(:,l,3,1))) .dot. bond) + (r_m_cross_r_l .dot. ((/ 0.0_dp, 0.0_dp, 1.0_dp /) - (bond * bond(3) / bond_len**2)))) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,1,2) = (dr(:,m,1,2) .dot. r(:,l)) + (r(:,m) .dot. dr(:,l,1,2))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,2,2) = (dr(:,m,2,2) .dot. r(:,l)) + (r(:,m) .dot. dr(:,l,2,2))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,3,2) = (dr(:,m,3,2) .dot. r(:,l)) + (r(:,m) .dot. dr(:,l,3,2))
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),1,2) = ((((dr(:,m,1,2) .cross. r(:,l)) + (r(:,m) .cross. dr(:,l,1,2))) .dot. bond) + (r_m_cross_r_l .dot. ((/ -1.0_dp, 0.0_dp, 0.0_dp /) + (bond * bond(1) / bond_len**2)))) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),2,2) = ((((dr(:,m,2,2) .cross. r(:,l)) + (r(:,m) .cross. dr(:,l,2,2))) .dot. bond) + (r_m_cross_r_l .dot. ((/ 0.0_dp, -1.0_dp, 0.0_dp /) + (bond * bond(2) / bond_len**2)))) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),3,2) = ((((dr(:,m,3,2) .cross. r(:,l)) + (r(:,m) .cross. dr(:,l,3,2))) .dot. bond) + (r_m_cross_r_l .dot. ((/ 0.0_dp, 0.0_dp, -1.0_dp /) + (bond * bond(3) / bond_len**2)))) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,1,m) = dr(:,m,1,m) .dot. r(:,l)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,2,m) = dr(:,m,2,m) .dot. r(:,l)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,3,m) = dr(:,m,3,m) .dot. r(:,l)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),1,m) = ((dr(:,m,1,m) .cross. r(:,l)) .dot. bond) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),2,m) = ((dr(:,m,2,m) .cross. r(:,l)) .dot. bond) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),3,m) = ((dr(:,m,3,m) .cross. r(:,l)) .dot. bond) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,1,l) = r(:,m) .dot. dr(:,l,1,l)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,2,l) = r(:,m) .dot. dr(:,l,2,l)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l) - 1,3,l) = r(:,m) .dot. dr(:,l,3,l)
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),1,l) = ((r(:,m) .cross. dr(:,l,1,l)) .dot. bond) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),2,l) = ((r(:,m) .cross. dr(:,l,2,l)) .dot. bond) / bond_len
descriptor_out%x(i_desc)%grad_data(2 + ij_neighbours + (2 * (m - 1) * ij_neighbours) + (2 * l),3,l) = ((r(:,m) .cross. dr(:,l,3,l)) .dot. bond) / bond_len
endif
if(l < m) then
dself_overlap(:,m) = dself_overlap(:,m) + 2.0_dp * dc(m,:,m) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ c(m) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
* (pos(:,l) - pos(:,m)) / this%atom_sigma**2
if(l == 1) then
dself_overlap(:,1) = dself_overlap(:,1) + 2.0_dp * dc(m,:,1) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(l,:,1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ c(m) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
* (pos(:,m) - pos(:,l)) / this%atom_sigma**2
dself_overlap(:,2) = dself_overlap(:,2) + 2.0_dp * dc(m,:,2) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(l,:,2) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 )
elseif(l == 2) then
dself_overlap(:,1) = dself_overlap(:,1) + 2.0_dp * dc(m,:,1) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(l,:,1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 )
dself_overlap(:,2) = dself_overlap(:,2) + 2.0_dp * dc(m,:,2) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(l,:,2) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ c(m) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
* (pos(:,m) - pos(:,l)) / this%atom_sigma**2
else
dself_overlap(:,1) = dself_overlap(:,1) + 2.0_dp * dc(m,:,1) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(l,:,1) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 )
dself_overlap(:,2) = dself_overlap(:,2) + 2.0_dp * dc(m,:,2) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ 2.0_dp * c(m) * dc(l,:,2) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 )
dself_overlap(:,l) = dself_overlap(:,l) + 2.0_dp * c(m) * dc(l,:,l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
+ c(m) * c(l) * exp( -0.25_dp * normsq(pos(:,m) - pos(:,l)) / this%atom_sigma**2 ) \
* (pos(:,m) - pos(:,l)) / this%atom_sigma**2
endif
endif
enddo
endif
enddo
!descriptor_out%x(i_desc)%grad_data(1,:,:) = 0.0_dp
descriptor_out%x(i_desc)%grad_data(2,:,:) = dself_overlap
descriptor_out%x(i_desc)%grad_data(3:ij_neighbours + 2,:,:) = dc
descriptor_out%x(i_desc)%ii = ii
descriptor_out%x(i_desc)%pos = pos
descriptor_out%x(i_desc)%grad_covariance_cutoff = 0.0_dp
descriptor_out%x(i_desc)%grad_covariance_cutoff(:,1) = dcoordination_function(r_ij, this%bond_cutoff, this%bond_transition_width) * bond / r_ij
descriptor_out%x(i_desc)%grad_covariance_cutoff(:,2) = - descriptor_out%x(i_desc)%grad_covariance_cutoff(:,1)
descriptor_out%x(i_desc)%has_grad_data = .true.
endif
if(my_do_descriptor .or. my_do_grad_descriptor) then
deallocate(r, z, c)
deallocate(ii, pos)
if(my_do_grad_descriptor) then
deallocate(dr, dz, dc, dself_overlap)
endif
endif
call finalise(at_copy)
enddo
enddo
call system_timer('bond_real_space_calc')
endsubroutine bond_real_space_calc
function bond_real_space_dimensions(this,error) result(i)
type(bond_real_space), intent(in) :: this
integer, optional, intent(out) :: error
integer :: i
INIT_ERROR(error)
if(.not. this%initialised) then
RAISE_ERROR("bond_real_space_dimensions: descriptor object not initialised", error)
endif
i = 2 + (1 + 2 * this%max_neighbours) * this%max_neighbours
endfunction bond_real_space_dimensions
function bond_real_space_cutoff(this,error)
type(bond_real_space), intent(in) :: this
integer, optional, intent(out) :: error
real(dp) :: bond_real_space_cutoff
INIT_ERROR(error)
if(.not. this%initialised) then
RAISE_ERROR("bond_real_space_cutoff: descriptor object not initialised", error)
endif
bond_real_space_cutoff = max(this%cutoff, this%bond_cutoff)
endfunction bond_real_space_cutoff
subroutine bond_real_space_sizes(this,at,n_descriptors,n_cross,mask,n_index,error)
type(bond_real_space), intent(in) :: this
type(atoms), intent(in) :: at
integer, intent(out) :: n_descriptors, n_cross
logical, dimension(:), intent(in), optional :: mask
integer, intent(out), optional :: n_index
integer, optional, intent(out) :: error
type(atoms) :: at_copy
integer :: i, j, k, n, m, shift_j(3)
INIT_ERROR(error)
if(.not. this%initialised) then
RAISE_ERROR("bond_real_space_sizes: descriptor object not initialised", error)
endif
n_descriptors = 0
n_cross = 0
do i = 1, at%N
n_descriptors = n_descriptors + n_neighbours(at, i, max_dist=this%bond_cutoff)
do n = 1, n_neighbours(at, i)
j = neighbour(at, i, n, shift=shift_j, max_dist=this%bond_cutoff)
if(j == 0) cycle
at_copy = at
call add_atoms(at_copy, 0.5_dp * (at%pos(:,i) + at%pos(:,j) + matmul(at%lattice,shift_j)), 1)
call calc_connect(at_copy)
do m = 1, n_neighbours(at_copy, at%N + 1)
k = neighbour(at_copy, at%N + 1, m, max_dist=this%cutoff)
if(k == 0) cycle
if(at_copy%pos(:,k) .feq. at_copy%pos(:,at%N + 1)) cycle
n_cross = n_cross + 1
enddo
call finalise(at_copy)
enddo
enddo
if( present(n_index) ) n_index = 2
endsubroutine bond_real_space_sizes
!!!!!!!!
!!! Work of Wojciech Szlachta ENDS here
!!!!!!!!
!!!!!!!!
!!! Work of Alan Nichol and S. T. John BEGINS here
!!!!!!!!
subroutine descriptor_general_monomer_nmer_MPI_setup(this,at,mpi,mpi_mask,error)
type(descriptor), intent(in) :: this
type(atoms), intent(in) :: at
type(MPI_Context), intent(in) :: mpi
logical, dimension(:), intent(out) :: mpi_mask
integer, optional, intent(out) :: error
integer, dimension(:,:), allocatable :: monomer_index
logical, dimension(at%N) :: associated_to_monomer
integer :: n_monomer
integer :: i
INIT_ERROR(error)
associated_to_monomer = .false.
select case(this%descriptor_type)
case(DT_GENERAL_MONOMER)
call find_general_monomer(at, monomer_index, &
this%descriptor_general_monomer%signature, associated_to_monomer, &
this%descriptor_general_monomer%cutoff, &
this%descriptor_general_monomer%atom_ordercheck, error)
case(DT_GENERAL_DIMER)
call find_general_monomer(at, monomer_index, &
this%descriptor_general_dimer%signature_one, associated_to_monomer, &
this%descriptor_general_dimer%monomer_one_cutoff, &
this%descriptor_general_dimer%atom_ordercheck, error)
case(DT_GENERAL_TRIMER)
call find_general_monomer(at, monomer_index, &
this%descriptor_general_trimer%signature_one, associated_to_monomer, &
this%descriptor_general_trimer%monomer_one_cutoff,&
this%descriptor_general_trimer%atom_ordercheck,error)
case(DT_COM_DIMER)
call find_general_monomer(at, monomer_index, &
this%descriptor_com_dimer%signature_one, associated_to_monomer,&
this%descriptor_com_dimer%monomer_one_cutoff,&
this%descriptor_com_dimer%atom_ordercheck,error)
case default
RAISE_ERROR("descriptor_general_monomer_nmer_MPI_setup: descriptor type "//this%descriptor_type//" not recognised.",error)
endselect
n_monomer = size(monomer_index,2)
mpi_mask = .false.
do i = 1, n_monomer ! for dimer, trimer this is the first monomer (signature_one)
if( mod(i-1, mpi%n_procs) == mpi%my_proc ) then
mpi_mask(monomer_index(:,i)) = .true.
endif
enddo
deallocate(monomer_index)
endsubroutine descriptor_general_monomer_nmer_MPI_setup
subroutine AN_monomer_initialise(this,args_str,error)
type(AN_monomer), intent(inout) :: this
character(len=*), intent(in) :: args_str
integer, optional, intent(out) :: error
type(Dictionary) :: params
INIT_ERROR(error)
call finalise(this)
call initialise(params)
call param_register(params, 'cutoff', '0.00', this%cutoff, help_string="Cutoff for AN_monomer-type descriptors")
call param_register(params, 'atomic_number', '1', this%atomic_number, help_string="Atomic number in AN_monomer-type descriptors")
call param_register(params, 'N', '4', this%N, help_string="Number of atoms in cluster")
call param_register(params, 'do_atomic', 'T', this%do_atomic, help_string="Descriptors are cluster based or atom-based")
if (.not. param_read_line(params, args_str, ignore_unknown=.true.,task='AN_monomer_initialise args_str')) then
RAISE_ERROR("AN_monomer_initialise failed to parse args_str='"//trim(args_str)//"'", error)
endif
call finalise(params)
this%initialised = .true.
endsubroutine AN_monomer_initialise
subroutine AN_monomer_finalise(this,error)
type(AN_monomer), intent(inout) :: this
integer, optional, intent(out) :: error
INIT_ERROR(error)
if(.not. this%initialised) return
this%cutoff = 0.0_dp
this%atomic_number = 0
this%N = 0
this%do_atomic = .false.
this%initialised = .false.
endsubroutine AN_monomer_finalise
subroutine general_monomer_initialise(this,args_str,error)
type(general_monomer), intent(inout) :: this
character(len=*), intent(in) :: args_str
character(len=STRING_LENGTH) :: signature_string
character(len=STRING_LENGTH_SHORT), dimension(99) :: signature_fields
integer, optional, intent(out) :: error
integer :: i,n_atoms,j
type(Dictionary) :: params
INIT_ERROR(error)
call finalise(this)
call initialise(params)
call param_register(params, 'cutoff', '0.00', this%cutoff, help_string="Cutoff for general_monomer-type descriptors")
call param_register(params, 'signature', PARAM_MANDATORY, signature_string, help_string="Atomic numbers of monomer one, format {Z1 Z2 Z3 ...}")
call param_register(params, 'atom_ordercheck', 'true', this%atom_ordercheck, help_string="T: find molecules. F: go by order of atoms")
call param_register(params, 'strict', 'true', this%strict, help_string="Raise error if not all atoms assigned to monomer")
call param_register(params, 'power', '1.0', this%power, help_string="Power of distances to be used in the kernel")
if (.not. param_read_line(params, args_str, ignore_unknown=.true.,task='general_monomer_initialise args_str')) then
RAISE_ERROR("general_monomer_initialise failed to parse args_str='"//trim(args_str)//"'", error)
endif
call finalise(params)
call split_string(signature_string,' ','{}',signature_fields(:),n_atoms,matching=.true.)
allocate(this%signature(n_atoms))
do i=1,n_atoms
this%signature(i) = string_to_int(signature_fields(i))
end do
call permutation_data_initialise(this%permutation_data,signature_one=this%signature,error=error)
this%initialised = .true.
endsubroutine general_monomer_initialise
subroutine general_monomer_finalise(this,error)
type(general_monomer), intent(inout) :: this
integer, optional, intent(out) :: error
INIT_ERROR(error)
if(.not. this%initialised) return
this%cutoff = 0.0_dp
this%power = 1.0_dp
if(allocated(this%signature)) deallocate(this%signature)
this%initialised = .false.
endsubroutine general_monomer_finalise
subroutine com_dimer_initialise(this,args_str,error)
type(com_dimer), intent(inout) :: this
character(len=*), intent(in) :: args_str
character(len=STRING_LENGTH) :: signature_one_string, signature_two_string
character(len=STRING_LENGTH_SHORT), dimension(99) :: signature_one_fields, signature_two_fields
integer, optional, intent(out) :: error
integer :: i, n_atoms_one, n_atoms_two
type(Dictionary) :: params
INIT_ERROR(error)
call finalise(this)
call initialise(params)
call param_register(params, 'cutoff', '0.00', this%cutoff, help_string="Cutoff(intermolecular) for com_dimer-type descriptors")
call param_register(params, 'monomer_one_cutoff', '0.00', this%monomer_one_cutoff, help_string="Cutoff(mono1) for com_dimer-type descriptors")
call param_register(params, 'monomer_two_cutoff', '0.00', this%monomer_two_cutoff, help_string="Cutoff(mono2) for com_dimer-type descriptors")
call param_register(params, 'cutoff_transition_width', '0.50', this%cutoff_transition_width, help_string="Width of smooth cutoff region for com_dimer-type descriptors")
call param_register(params, 'atom_ordercheck', 'true', this%atom_ordercheck, help_string="T: find molecules. F: go by order of atoms")
call param_register(params, 'strict', 'true', this%strict, help_string="Raise error if not all atoms assigned to monomer or if no monomer pairs found")
call param_register(params, 'mpifind', 'false', this%mpifind, help_string="Use find_monomer_pairs_MPI")
call param_register(params, 'signature_one', PARAM_MANDATORY, signature_one_string, help_string="Atomic numbers of monomer one, format {Z1 Z2 Z3 ...}")
call param_register(params, 'signature_two', PARAM_MANDATORY, signature_two_string, help_string="Atomic numbers of monomer two, format {Z1 Z2 Z3 ...}")
if (.not. param_read_line(params, args_str, ignore_unknown=.true.,task='com_dimer_initialise args_str')) then
RAISE_ERROR("com_dimer_initialise failed to parse args_str='"//trim(args_str)//"'", error)
endif
call finalise(params)
call initialise(this%transfer_parameters, args_str, error)
call split_string(signature_one_string,' ','{}',signature_one_fields(:),n_atoms_one,matching=.true.)
call split_string(signature_two_string,' ','{}',signature_two_fields(:),n_atoms_two,matching=.true.)
allocate(this%signature_one(n_atoms_one))
allocate(this%signature_two(n_atoms_two))
do i=1,n_atoms_one
this%signature_one(i) = string_to_int(signature_one_fields(i))
end do
do i=1,n_atoms_two
this%signature_two(i) = string_to_int(signature_two_fields(i))
end do
this%monomers_identical=.False.
if (size(this%signature_one) == size(this%signature_two)) then
if (all(this%signature_one == this%signature_two)) then
this%monomers_identical = .True.
end if
end if
this%initialised = .true.
endsubroutine com_dimer_initialise
subroutine com_dimer_finalise(this,error)
type(com_dimer), intent(inout) :: this
integer, optional, intent(out) :: error
INIT_ERROR(error)
if(.not. this%initialised) return
this%cutoff = 0.0_dp
this%cutoff_transition_width = 0.0_dp
this%monomer_one_cutoff = 0.0_dp
this%monomer_two_cutoff = 0.0_dp
this%atom_ordercheck = .true.
this%use_smooth_cutoff = .false.
if(allocated(this%signature_one)) deallocate(this%signature_one)
if(allocated(this%signature_two)) deallocate(this%signature_two)
this%initialised = .false.
endsubroutine com_dimer_finalise
subroutine general_dimer_initialise(this,args_str,error)
type(general_dimer), intent(inout) :: this
character(len=*), intent(in) :: args_str
character(len=STRING_LENGTH) :: signature_one_string, signature_two_string
character(len=STRING_LENGTH_SHORT), dimension(99) :: signature_one_fields, signature_two_fields
integer, optional, intent(out) :: error
integer :: i,j, n_atoms_one, n_atoms_two, dimer_size, start, finish, d
logical, dimension(:,:), allocatable :: intermolecular
integer, dimension(:), allocatable :: signature
type(Dictionary) :: params
INIT_ERROR(error)
call finalise(this)
call initialise(params)
call param_register(params, 'cutoff', '0.00', this%cutoff, &
help_string="Cutoff(intermolecular) for general_dimer-type descriptors")
call param_register(params, 'monomer_one_cutoff', '0.00', this%monomer_one_cutoff, &
help_string="Cutoff(mono1) for general_dimer-type descriptors")
call param_register(params, 'monomer_two_cutoff', '0.00', this%monomer_two_cutoff, &
help_string="Cutoff(mono2) for general_dimer-type descriptors")
call param_register(params, 'cutoff_transition_width', '0.50', this%cutoff_transition_width, &
help_string="Width of smooth cutoff region for general_dimer-type descriptors")
call param_register(params, 'internal_swaps_only', 'true', this%internal_swaps_only, &
help_string="F: energies will be symmetrised over swaps of nuclei between monomers")
call param_register(params, 'atom_ordercheck', 'true', this%atom_ordercheck, &
help_string="T: find molecules. F: go by order of atoms")
call param_register(params, 'double_count', 'false', this%double_count, &
help_string="T: double count when constructing the dimers, for compatibility with water dimer descriptor, default False")
call param_register(params, 'strict', 'true', this%strict, &
help_string="Raise error if not all atoms assigned to monomer or if no monomer pairs found")
call param_register(params, 'strict_mask', 'true', this%strict_mask, &
help_string="Raise error if atom mask includes only part of a monomer")
call param_register(params, 'use_com', 'false', this%use_com, &
help_string="Use COM instead of COG")
call param_register(params, 'mpifind', 'false', this%mpifind, &
help_string="Use find_monomer_pairs_MPI")
call param_register(params, 'signature_one', PARAM_MANDATORY, signature_one_string, &
help_string="Atomic numbers of monomer one, format {Z1 Z2 Z3 ...}")
call param_register(params, 'signature_two', PARAM_MANDATORY, signature_two_string, &
help_string="Atomic numbers of monomer two, format {Z1 Z2 Z3 ...}")
call param_register(params, 'power', '1.00', this%power, &
help_string="Power of interatomic distances to be used in the kernel.")
call param_register(params, 'dist_shift', '0.0', this%dist_shift, &
help_string="Distance shift for inverse distance descriptors.")
if (.not. param_read_line(params, args_str, ignore_unknown=.true.,task='general_dimer_initialise args_str')) then
RAISE_ERROR("general_dimer_initialise failed to parse args_str='"//trim(args_str)//"'", error)
endif
call finalise(params)
call initialise(this%transfer_parameters, args_str, error)
call split_string(signature_one_string,' ','{}',signature_one_fields(:),n_atoms_one,matching=.true.)
call split_string(signature_two_string,' ','{}',signature_two_fields(:),n_atoms_two,matching=.true.)
allocate(this%signature_one(n_atoms_one))
allocate(this%signature_two(n_atoms_two))
do i=1,n_atoms_one
this%signature_one(i) = string_to_int(signature_one_fields(i))
end do
do i=1,n_atoms_two
this%signature_two(i) = string_to_int(signature_two_fields(i))
end do
this%monomers_identical=.False.
if (size(this%signature_one) == size(this%signature_two)) then
if (all(this%signature_one == this%signature_two)) then
this%monomers_identical = .True.
end if
end if
call permutation_data_initialise(this%permutation_data,signature_one=this%signature_one,signature_two=this%signature_two,internal_swaps_only=this%internal_swaps_only,error=error)
dimer_size=n_atoms_one + n_atoms_two
d=dimer_size*(dimer_size-1)/2
allocate(signature(dimer_size))
allocate(intermolecular(dimer_size,dimer_size))
allocate(this%is_intermolecular(d))
allocate(this%cutoff_contributor(d))
allocate(this%component_atoms(d,2))
signature(1:n_atoms_one) = this%signature_one
signature(1+n_atoms_one:dimer_size) = this%signature_two
intermolecular = .false.
this%cutoff_contributor=.false.
do i=1,n_atoms_one
do j=1+n_atoms_one,dimer_size
intermolecular(i,j)=.true.
end do
end do
start = 0
finish=dimer_size-1
do i=1,dimer_size
do j=1,finish-start
this%is_intermolecular(start+j) = intermolecular(i,i+j)
this%component_atoms(start+j,:) = (/ i, i+j /)
end do
start = finish
finish=finish + dimer_size-i-1
end do
do i=1,d
if (this%is_intermolecular(i)) then
if (.not. signature(this%component_atoms(i,1))==1 ) then
if (.not. signature(this%component_atoms(i,2))==1 ) then
this%cutoff_contributor(i)=.true.
end if
end if
end if
end do
this%initialised = .true.
deallocate(signature)
deallocate(intermolecular)
endsubroutine general_dimer_initialise
subroutine general_dimer_finalise(this,error)
type(general_dimer), intent(inout) :: this
integer, optional, intent(out) :: error
INIT_ERROR(error)
if(.not. this%initialised) return
this%cutoff = 0.0_dp
this%cutoff_transition_width = 0.0_dp
this%monomer_one_cutoff = 0.0_dp
this%monomer_two_cutoff = 0.0_dp
this%atom_ordercheck = .true.
this%internal_swaps_only = .true.
this%use_smooth_cutoff = .false.
this%power = 1.0_dp
this%dist_shift = 0.0_dp
if(allocated(this%signature_one)) deallocate(this%signature_one)
if(allocated(this%signature_two)) deallocate(this%signature_two)
if(allocated(this%is_intermolecular)) deallocate(this%is_intermolecular)
if(allocated(this%component_atoms)) deallocate(this%component_atoms)
if(allocated(this%cutoff_contributor)) deallocate(this%cutoff_contributor)
this%initialised = .false.
endsubroutine general_dimer_finalise
subroutine general_trimer_initialise(this,args_str,error)
type(general_trimer), intent(inout) :: this
character(len=*), intent(in) :: args_str
character(len=STRING_LENGTH) :: signature_one_string, signature_two_string, signature_three_string
character(len=STRING_LENGTH_SHORT), dimension(99) :: signature_one_fields, signature_two_fields, signature_three_fields
integer, optional, intent(out) :: error
integer :: i,j, n_atoms_one, n_atoms_two, n_atoms_three, trimer_size, start, finish,d
logical, dimension(:,:), allocatable :: intermolecular
integer, dimension(:), allocatable :: signature
type(Dictionary) :: params
INIT_ERROR(error)
call finalise(this)
call initialise(params)
call param_register(params, 'cutoff', '0.00', this%cutoff, &
help_string="Cutoff(intermolecular) for general_trimer-type descriptors")
call param_register(params, 'monomer_one_cutoff', '0.00', this%monomer_one_cutoff, &
help_string="Cutoff(mono1) for general_trimer-type descriptors")
call param_register(params, 'monomer_two_cutoff', '0.00', this%monomer_two_cutoff, &
help_string="Cutoff(mono2) for general_trimer-type descriptors")
call param_register(params, 'monomer_three_cutoff', '0.00', this%monomer_three_cutoff, &
help_string="Cutoff(mono3) for general_trimer-type descriptors")
call param_register(params, 'cutoff_transition_width', '0.50', this%cutoff_transition_width, &
help_string="Width of smooth cutoff region for general_trimer-type descriptors")
call param_register(params, 'internal_swaps_only', 'true', this%internal_swaps_only, &
help_string="F: energies will be symmetrised over swaps of nuclei between monomers")
call param_register(params, 'atom_ordercheck', 'true', this%atom_ordercheck, &
help_string="T: find molecules. F: go by order of atoms")
call param_register(params, 'strict', 'true', this%strict, &
help_string="Raise error if not all atoms assigned to monomer or if no monomer pairs found")
call param_register(params, 'use_com', 'false', this%use_com, &
help_string="Use COM instead of COG")
call param_register(params, 'mpifind', 'false', this%mpifind, &
help_string="Use find_monomer_triplets_MPI")
call param_register(params, 'signature_one', PARAM_MANDATORY, signature_one_string, &
help_string="Atomic numbers of monomer one, format {Z1 Z2 Z3 ...}")
call param_register(params, 'signature_two', PARAM_MANDATORY, signature_two_string, &
help_string="Atomic numbers of monomer two, format {Z1 Z2 Z3 ...}")
call param_register(params, 'signature_three', PARAM_MANDATORY, signature_three_string, &
help_string="Atomic numbers of monomer three, format {Z1 Z2 Z3 ...}")
call param_register(params, 'power', '1.0', this%power, &
help_string="Power of distances to be used in the kernel")
call param_register(params, 'dist_shift', '0.0', this%dist_shift, &
help_string="Distance shift for inverse distance descriptors.")
if (.not. param_read_line(params, args_str, ignore_unknown=.true.,task='general_trimer_initialise args_str')) then