-
Notifications
You must be signed in to change notification settings - Fork 19
/
descriptors_noncommercial_permutations.inc
175 lines (147 loc) · 8.13 KB
/
descriptors_noncommercial_permutations.inc
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
! 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_WATER_TRIMER)
if (.not. this%descriptor_water_trimer%permutation_data%initialised)then
RAISE_ERROR("descriptor_permutations: permutation_data not initialised "//this%descriptor_type,error)
else if (this%descriptor_water_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_water_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