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descriptors_noncommercial_permutations.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
!
!
! This file contains descriptors written by others, not A. P. Bartok and Gabor Csanyi
! and the code here is owned by their respective authors, as indicated below.
!
!
! Author: Alan Nichol
!
case(DT_AN_MONOMER)
allocate(distance_matrix(this%descriptor_AN_monomer%N,this%descriptor_AN_monomer%N), atom_permutations(this%descriptor_AN_monomer%N,np))
if(this%descriptor_AN_monomer%do_atomic) then
atom_permutations(1,:) = 0
call generate_AN_permutations(atom_permutations(2:this%descriptor_AN_monomer%N,:))
atom_permutations = atom_permutations + 1
else
call generate_AN_permutations(atom_permutations(:,:))
endif
i = 0
distance_matrix = 0
do n = 2, this%descriptor_AN_monomer%N
i = i + 1
distance_matrix(1,n) = i
distance_matrix(n,1) = i
do m = n+1, this%descriptor_AN_monomer%N
i = i + 1
distance_matrix(m,n) = i
distance_matrix(n,m) = i
enddo
enddo
do ip = 1, np
i = 0
do n = 2, this%descriptor_AN_monomer%N
i = i + 1
permutations(i,ip) = distance_matrix(atom_permutations(1,ip),atom_permutations(n,ip))
do m = n+1, this%descriptor_AN_monomer%N
i = i + 1
permutations(i,ip) = distance_matrix(atom_permutations(m,ip),atom_permutations(n,ip))
enddo
enddo
enddo
deallocate(distance_matrix,atom_permutations)
case(DT_GENERAL_MONOMER)
if (.not. this%descriptor_general_monomer%permutation_data%initialised) then
RAISE_ERROR("descriptor_permutations: permutation_data not initialised "//this%descriptor_type,error)
else if (this%descriptor_general_monomer%permutation_data%perm_number /= 1) then
RAISE_ERROR("descriptor_permutations: permutation_data%perm_number must be initialised to one"//this%descriptor_type,error)
end if
call permutation_data_copy(my_permutation_data, this%descriptor_general_monomer%permutation_data)
if (my_permutation_data%n_perms > 1) then
call next(my_permutation_data, 1)
end if
permutations=my_permutation_data%dist_vec_permutations
case(DT_GENERAL_DIMER)
if (.not. this%descriptor_general_dimer%permutation_data%initialised)then
RAISE_ERROR("descriptor_permutations: permutation_data not initialised "//this%descriptor_type,error)
else if (this%descriptor_general_dimer%permutation_data%perm_number /= 1) then
RAISE_ERROR("descriptor_permutations: permutation_data%perm_number must be initialised to one"//this%descriptor_type,error)
end if
call permutation_data_copy(my_permutation_data, this%descriptor_general_dimer%permutation_data)
if (my_permutation_data%n_perms > 1) then
call next(my_permutation_data, 1)
end if
permutations=my_permutation_data%dist_vec_permutations
case(DT_GENERAL_TRIMER)
if (.not. this%descriptor_general_trimer%permutation_data%initialised)then
RAISE_ERROR("descriptor_permutations: permutation_data not initialised "//this%descriptor_type,error)
else if (this%descriptor_general_trimer%permutation_data%perm_number /= 1) then
RAISE_ERROR("descriptor_permutations: permutation_data%perm_number must be initialised to one"//this%descriptor_type,error)
end if
call permutation_data_copy(my_permutation_data, this%descriptor_general_trimer%permutation_data)
if (my_permutation_data%n_perms > 1) then
call next(my_permutation_data, 1)
end if
permutations=my_permutation_data%dist_vec_permutations
case(DT_MOLECULE_LO_D)
if (.not. this%descriptor_molecule_lo_d%permutation_data%initialised) then
RAISE_ERROR("descriptor_permutations: permutation_data not initialised "//this%descriptor_type,error)
else if (this%descriptor_molecule_lo_d%permutation_data%perm_number /= 1) then
RAISE_ERROR("descriptor_permutations: permutation_data%perm_number must be initialised to one"//this%descriptor_type,error)
end if
call permutation_data_copy(my_permutation_data, this%descriptor_molecule_lo_d%permutation_data)
if (my_permutation_data%n_perms > 1) then
call next(my_permutation_data, 1)
end if
allocate(sliced_permutations(size(this%descriptor_molecule_lo_d%included_components),my_permutation_data%n_perms))
allocate(this_perm(size(this%descriptor_molecule_lo_d%included_components)))
sliced_permutations =my_permutation_data%dist_vec_permutations(this%descriptor_molecule_lo_d%included_components,:)
do j=1,my_permutation_data%n_perms
this_perm=sliced_permutations(:,j)
do i=1,size(this%descriptor_molecule_lo_d%included_components)
unit_vec=maxloc(this%descriptor_molecule_lo_d%included_components, mask=this%descriptor_molecule_lo_d%included_components .eq. this_perm(i))
if (unit_vec(1) == 0) then
RAISE_ERROR("descriptor_permutations: you have specified symmetries between atoms with different connectivity",error)
end if
permutations(i,j) =unit_vec(1)
end do
end do
! begin brau
if(size(this%descriptor_molecule_lo_d%included_components) > maxval(this%descriptor_molecule_lo_d%included_components)) then
permutations=my_permutation_data%dist_vec_permutations
end if
! end brau