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remove obsolete reax tools and rename pair_meam.txt to pair_meamc.txt

This commit is contained in:
Axel Kohlmeyer 2018-12-10 14:16:08 -05:00
parent 93efe3e40e
commit dedc6cf20c
4 changed files with 0 additions and 1817 deletions
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0
doc/src/pair_meam.txt → doc/src/pair_meamc.txt
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232
tools/reax/bondConnectCheck.f90
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@ -1,232 +0,0 @@
!# DEC.9, 2010
!# HLL
!# NCSU
!#
!# This is a program to read the output from 'fix reax/bond', TPRD, Lammps
!# The output is saved into file "bonds.reax", where each image is divided
!# into three parts:
!#
!# (1) Head, 7 Lines;
!# (2) Body, No._of_atom Lines;
!# (3) Tail, 1 Line
!#
!# The total number of images is related with the output frequence and number of iterations.
!# In this case, it is "number of iteration+1".
!#
!# Each line in Body part is made up of the following parameters:
!# id, type, nb, id_1, id_2, ... id_nb, mol, bo_1, bo_2, ... bo_nb, abo, nlp, q
!# abo = atomic bond order
!# nlp = number of lone pairs
!# q = atomic charge
!#
!# PLEASE DOUBLE CHECK YOUR OWN LAMMPS INPUT SCRIPT & OUTPUT AND MAKE CORRESPONDING CHSNGES
program main
implicit none
integer I, J, K, L
integer image, natom
integer headline, tailline
integer id, atype, nb, bd1, bd2, bd3, bd4, mol
double precision bo1, bo2, bo3, bo4, abo, nlp, q
open (unit=10, file='bonds.reax')
open (unit=20, file='N129.txt', status='unknown')
open (unit=21, file='N133.txt', status='unknown')
open (unit=22, file='N137.txt', status='unknown')
open (unit=23, file='N141.txt', status='unknown')
open (unit=24, file='N145.txt', status='unknown')
open (unit=25, file='N149.txt', status='unknown')
open (unit=26, file='N153.txt', status='unknown')
open (unit=27, file='N157.txt', status='unknown')
open (unit=30, file='reactionRecord.txt', status='unknown')
!# Make changes accordingly.
image = 1
headline = 7
tailline = 1
natom = 384
do I = 1, image+1
! Skip the head part
do J = 1, headline
read(10,*)
end do
! Each image has 'natom' lines
do K = 1, natom
! read in the first three number each line to determine:
! (1) what type of atom it is, atype
! the correspondence in Lammps: 1-C, 2-H, 3-O, 4-N, 5-S
! (2) how many bonds it has, nb
! this 'nb' determines the following bond_link information & bond_order paramaters of the same line
read(10,*) id, atype, nb
! TEST
! write(*,*) id, atype, nb
if (atype .eq. 4) then
backspace 10
! Should have some easier way to replace this "IF", I am just toooo lazy.
! Thanks to the fact that the maximum number of bonds is 4. ^-^
!??? is it possible that nb = 0 ??? KEEP THAT IN MIND.
if (nb.eq.0) then
read(10,*) id, atype, nb, mol, abo, nlp, q
if (id .eq. 129) then
write(20, 200) id, atype, nb, mol, abo, nlp, q
elseif (id .eq. 133) then
write(21, 200) id, atype, nb, mol, abo, nlp, q
elseif (id .eq. 137) then
write(22, 200) id, atype, nb, mol, abo, nlp, q
elseif (id .eq. 141) then
write(23, 200) id, atype, nb, mol, abo, nlp, q
elseif (id .eq. 145) then
write(24, 200) id, atype, nb, mol, abo, nlp, q
elseif (id .eq. 149) then
write(25, 200) id, atype, nb, mol, abo, nlp, q
elseif (id .eq. 153) then
write(26, 200) id, atype, nb, mol, abo, nlp, q
elseif (id .eq. 157) then
write(27, 200) id, atype, nb, mol, abo, nlp, q
200 format(4I4, 3f14.3)
endif
! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
write (30, 300) I, id, atype, nb, mol, abo, nlp, q
300 format(5I4, 3f14.3)
elseif (nb.eq.1) then
read(10,*) id, atype, nb, bd1, mol, bo1, abo, nlp, q
if (id .eq. 129) then
write(20, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
elseif (id .eq. 133) then
write(21, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
elseif (id .eq. 137) then
write(22, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
elseif (id .eq. 141) then
write(23, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
elseif (id .eq. 145) then
write(24, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
elseif (id .eq. 149) then
write(25, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
elseif (id .eq. 153) then
write(26, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
elseif (id .eq. 157) then
write(27, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
201 format(5I4, 4f14.3)
endif
! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
write (30, 301) I, id, atype, nb, bd1, mol, bo1, abo, nlp, q
301 format(6I4, 4f14.3)
elseif (nb.eq.2) then
read(10,*) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
if (id .eq. 129) then
write(20, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
elseif (id .eq. 133) then
write(21, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
elseif (id .eq. 137) then
write(22, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
elseif (id .eq. 141) then
write(23, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
elseif (id .eq. 145) then
write(24, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
elseif (id .eq. 149) then
write(25, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
elseif (id .eq. 153) then
write(26, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
elseif (id .eq. 157) then
write(27, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
202 format(6I4, 5f14.3)
endif
! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
write (30, 302) I, id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
302 format(7I4, 5f14.3)
elseif (nb.eq.3) then
read(10,*) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
if (id .eq. 129) then
write(20, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
elseif (id .eq. 133) then
write(21, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
elseif (id .eq. 137) then
write(22, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
elseif (id .eq. 141) then
write(23, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
elseif (id .eq. 145) then
write(24, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
elseif (id .eq. 149) then
write(25, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
elseif (id .eq. 153) then
write(26, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bd3, abo, nlp, q
elseif (id .eq. 157) then
write(27, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
203 format(7I4, 6f14.3)
endif
elseif (nb.eq.4) then
read(10,*) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
if (id .eq. 129) then
write(20, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
elseif (id .eq. 133) then
write(21, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
elseif (id .eq. 137) then
write(22, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
elseif (id .eq. 141) then
write(23, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
elseif (id .eq. 145) then
write(24, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
elseif (id .eq. 149) then
write(25, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
elseif (id .eq. 153) then
write(26, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bd3, bo4, abo, nlp, q
elseif (id .eq. 157) then
write(27, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
204 format(8I4, 7f14.3)
endif
! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
write (30, 304) I, id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
304 format(9I4, 7f14.3)
! Corresponding to "if (nb.eq.0) then "
endif
! Corresponding to "if (atype .eq. 4) then"
endif
enddo
do L =1,tailline
read(10,*)
enddo
enddo
end program main

784
tools/reax/bonds.reax
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@ -1,784 +0,0 @@
# Timestep 0
#
# Number of particles 384
#
# Max.number of bonds per atom 3 with coarse bond order cutoff 0.300
# Particle connection table and bond orders
# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q
1 1 3 2 6 13 0 1.324 1.332 1.109 3.767 0.000 -0.073
2 1 3 1 3 14 0 1.324 1.345 1.300 3.969 0.000 0.193
3 1 3 2 4 15 0 1.345 1.336 1.083 3.767 0.000 -0.060
4 1 3 3 5 16 0 1.336 1.306 1.324 3.967 0.000 0.196
5 1 3 4 6 17 0 1.306 1.317 1.143 3.769 0.000 -0.063
6 1 3 1 5 18 0 1.332 1.317 1.318 3.967 0.000 0.191
7 2 1 14 0 0.873 1.075 0.000 0.366
8 2 1 14 0 0.897 1.056 0.000 0.386
9 2 1 16 0 0.905 1.051 0.000 0.379
10 2 2 16 23 0 0.838 0.267 1.105 0.000 0.385
11 2 2 18 24 0 0.868 0.216 1.083 0.000 0.377
12 2 1 18 0 0.881 1.069 0.000 0.386
13 4 3 1 20 19 0 1.109 1.198 1.197 3.504 0.165 0.344
14 4 3 2 7 8 0 1.300 0.873 0.897 3.070 0.966 -0.469
15 4 3 3 21 22 0 1.083 1.211 1.214 3.508 0.160 0.371
16 4 3 4 9 10 0 1.324 0.905 0.838 3.068 0.968 -0.443
17 4 3 5 23 24 0 1.143 1.171 1.190 3.504 0.165 0.341
18 4 3 6 11 12 0 1.318 0.868 0.881 3.067 0.969 -0.438
19 3 1 13 0 1.197 1.393 2.000 -0.381
20 3 1 13 0 1.198 1.407 2.000 -0.413
21 3 1 15 0 1.211 1.378 2.000 -0.375
22 3 1 15 0 1.214 1.368 2.000 -0.399
23 3 2 10 17 0 0.267 1.171 1.446 2.000 -0.388
24 3 2 11 17 0 0.216 1.190 1.413 2.000 -0.411
25 1 3 30 26 37 0 1.332 1.324 1.109 3.767 0.000 -0.073
26 1 3 25 27 38 0 1.324 1.345 1.300 3.969 0.000 0.193
27 1 3 26 28 39 0 1.345 1.336 1.083 3.767 0.000 -0.060
28 1 3 27 29 40 0 1.336 1.306 1.324 3.967 0.000 0.196
29 1 3 28 30 41 0 1.306 1.317 1.143 3.769 0.000 -0.063
30 1 3 25 29 42 0 1.332 1.317 1.318 3.967 0.000 0.191
31 2 1 38 0 0.873 1.075 0.000 0.366
32 2 1 38 0 0.897 1.056 0.000 0.386
33 2 1 40 0 0.905 1.051 0.000 0.379
34 2 2 47 40 0 0.267 0.838 1.105 0.000 0.385
35 2 2 42 48 0 0.868 0.216 1.083 0.000 0.377
36 2 1 42 0 0.881 1.069 0.000 0.386
37 4 3 25 43 44 0 1.109 1.197 1.198 3.504 0.165 0.344
38 4 3 26 32 31 0 1.300 0.897 0.873 3.070 0.966 -0.469
39 4 3 27 45 46 0 1.083 1.211 1.214 3.508 0.160 0.371
40 4 3 28 33 34 0 1.324 0.905 0.838 3.068 0.968 -0.443
41 4 3 29 47 48 0 1.143 1.171 1.190 3.504 0.165 0.341
42 4 3 30 35 36 0 1.318 0.868 0.881 3.067 0.969 -0.438
43 3 1 37 0 1.197 1.393 2.000 -0.381
44 3 1 37 0 1.198 1.407 2.000 -0.413
45 3 1 39 0 1.211 1.378 2.000 -0.375
46 3 1 39 0 1.214 1.368 2.000 -0.399
47 3 2 34 41 0 0.267 1.171 1.446 2.000 -0.388
48 3 2 35 41 0 0.216 1.190 1.413 2.000 -0.411
49 1 3 50 54 61 0 1.324 1.332 1.109 3.767 0.000 -0.073
50 1 3 49 51 62 0 1.324 1.345 1.300 3.969 0.000 0.193
51 1 3 50 52 63 0 1.345 1.336 1.083 3.767 0.000 -0.060
52 1 3 51 53 64 0 1.336 1.306 1.324 3.967 0.000 0.196
53 1 3 52 54 65 0 1.306 1.317 1.143 3.769 0.000 -0.063
54 1 3 49 53 66 0 1.332 1.317 1.318 3.967 0.000 0.191
55 2 1 62 0 0.873 1.075 0.000 0.366
56 2 1 62 0 0.897 1.056 0.000 0.386
57 2 1 64 0 0.905 1.051 0.000 0.379
58 2 2 64 71 0 0.838 0.267 1.105 0.000 0.385
59 2 2 66 72 0 0.868 0.216 1.083 0.000 0.377
60 2 1 66 0 0.881 1.069 0.000 0.386
62 4 3 50 55 56 0 1.300 0.873 0.897 3.070 0.966 -0.469
63 4 3 51 69 70 0 1.083 1.211 1.214 3.508 0.160 0.371
64 4 3 52 57 58 0 1.324 0.905 0.838 3.068 0.968 -0.443
65 4 3 53 71 72 0 1.143 1.171 1.190 3.504 0.165 0.341
66 4 3 54 59 60 0 1.318 0.868 0.881 3.067 0.969 -0.438
69 3 1 63 0 1.211 1.378 2.000 -0.375
70 3 1 63 0 1.214 1.368 2.000 -0.399
71 3 2 58 65 0 0.267 1.171 1.446 2.000 -0.388
72 3 2 59 65 0 0.216 1.190 1.413 2.000 -0.411
73 1 3 78 74 85 0 1.332 1.324 1.109 3.767 0.000 -0.073
74 1 3 73 75 86 0 1.324 1.345 1.300 3.969 0.000 0.193
75 1 3 74 76 87 0 1.345 1.336 1.083 3.767 0.000 -0.060
76 1 3 75 77 88 0 1.336 1.306 1.324 3.967 0.000 0.196
77 1 3 76 78 89 0 1.306 1.317 1.143 3.769 0.000 -0.063
78 1 3 73 77 90 0 1.332 1.317 1.318 3.967 0.000 0.191
79 2 1 86 0 0.873 1.075 0.000 0.366
80 2 1 86 0 0.897 1.056 0.000 0.386
81 2 1 88 0 0.905 1.051 0.000 0.379
82 2 2 95 88 0 0.267 0.838 1.105 0.000 0.385
83 2 2 90 96 0 0.868 0.216 1.083 0.000 0.377
84 2 1 90 0 0.881 1.069 0.000 0.386
85 4 3 73 91 92 0 1.109 1.197 1.198 3.504 0.165 0.344
86 4 3 74 80 79 0 1.300 0.897 0.873 3.070 0.966 -0.469
87 4 3 75 93 94 0 1.083 1.211 1.214 3.508 0.160 0.371
88 4 3 76 81 82 0 1.324 0.905 0.838 3.068 0.968 -0.443
89 4 3 77 95 96 0 1.143 1.171 1.190 3.504 0.165 0.341
90 4 3 78 83 84 0 1.318 0.868 0.881 3.067 0.969 -0.438
91 3 1 85 0 1.197 1.393 2.000 -0.381
92 3 1 85 0 1.198 1.407 2.000 -0.413
93 3 1 87 0 1.211 1.378 2.000 -0.375
94 3 1 87 0 1.214 1.368 2.000 -0.399
95 3 2 82 89 0 0.267 1.171 1.446 2.000 -0.388
96 3 2 83 89 0 0.216 1.190 1.413 2.000 -0.411
97 1 3 98 102 109 0 1.324 1.332 1.109 3.767 0.000 -0.073
98 1 3 97 99 110 0 1.324 1.345 1.300 3.969 0.000 0.193
99 1 3 98 100 111 0 1.345 1.337 1.083 3.767 0.000 -0.060
100 1 3 99 101 112 0 1.337 1.306 1.324 3.967 0.000 0.196
101 1 3 100 113 102 0 1.306 1.143 1.317 3.769 0.000 -0.063
102 1 3 97 101 114 0 1.332 1.317 1.318 3.967 0.000 0.191
103 2 1 110 0 0.873 1.075 0.000 0.366
104 2 1 110 0 0.897 1.056 0.000 0.386
105 2 1 112 0 0.905 1.051 0.000 0.379
106 2 2 119 112 0 0.267 0.838 1.105 0.000 0.385
107 2 2 114 120 0 0.868 0.216 1.083 0.000 0.377
108 2 1 114 0 0.881 1.069 0.000 0.386
109 4 3 116 97 115 0 1.198 1.109 1.197 3.504 0.165 0.344
110 4 3 103 104 98 0 0.873 0.897 1.300 3.070 0.966 -0.469
111 4 3 99 117 118 0 1.083 1.211 1.214 3.508 0.160 0.371
112 4 3 100 105 106 0 1.324 0.905 0.838 3.068 0.968 -0.443
113 4 3 101 119 120 0 1.143 1.171 1.190 3.504 0.165 0.341
114 4 3 102 107 108 0 1.318 0.868 0.881 3.067 0.969 -0.438
115 3 1 109 0 1.197 1.393 2.000 -0.381
116 3 1 109 0 1.198 1.407 2.000 -0.413
117 3 1 111 0 1.211 1.378 2.000 -0.375
118 3 1 111 0 1.214 1.368 2.000 -0.399
119 3 2 106 113 0 0.267 1.171 1.446 2.000 -0.388
120 3 2 107 113 0 0.216 1.190 1.413 2.000 -0.411
121 1 3 126 122 133 0 1.332 1.324 1.109 3.767 0.000 -0.073
122 1 3 121 123 134 0 1.324 1.345 1.300 3.969 0.000 0.193
123 1 3 122 124 135 0 1.345 1.336 1.083 3.767 0.000 -0.060
124 1 3 123 125 136 0 1.336 1.306 1.324 3.967 0.000 0.196
125 1 3 124 126 137 0 1.306 1.317 1.143 3.769 0.000 -0.063
126 1 3 121 125 138 0 1.332 1.317 1.318 3.967 0.000 0.191
127 2 1 134 0 0.873 1.075 0.000 0.366
128 2 1 134 0 0.897 1.056 0.000 0.386
129 2 1 136 0 0.905 1.051 0.000 0.379
130 2 2 143 136 0 0.267 0.838 1.105 0.000 0.385
131 2 2 138 144 0 0.868 0.216 1.083 0.000 0.377
132 2 1 138 0 0.881 1.069 0.000 0.386
133 4 3 121 139 140 0 1.109 1.197 1.198 3.504 0.165 0.344
134 4 3 122 127 128 0 1.300 0.873 0.897 3.070 0.966 -0.469
135 4 3 123 141 142 0 1.083 1.211 1.214 3.508 0.160 0.371
136 4 3 124 129 130 0 1.324 0.905 0.838 3.068 0.968 -0.443
137 4 3 125 143 144 0 1.143 1.171 1.190 3.504 0.165 0.341
138 4 3 126 131 132 0 1.318 0.868 0.881 3.067 0.969 -0.438
139 3 1 133 0 1.197 1.393 2.000 -0.381
140 3 1 133 0 1.198 1.407 2.000 -0.413
141 3 1 135 0 1.211 1.378 2.000 -0.375
142 3 1 135 0 1.214 1.368 2.000 -0.399
143 3 2 130 137 0 0.267 1.171 1.446 2.000 -0.388
144 3 2 131 137 0 0.216 1.190 1.413 2.000 -0.411
145 1 3 146 150 157 0 1.324 1.332 1.109 3.767 0.000 -0.073
146 1 3 145 147 158 0 1.324 1.345 1.300 3.969 0.000 0.193
147 1 3 146 148 159 0 1.345 1.337 1.083 3.767 0.000 -0.060
148 1 3 147 149 160 0 1.337 1.306 1.324 3.967 0.000 0.196
149 1 3 148 161 150 0 1.306 1.143 1.317 3.769 0.000 -0.063
150 1 3 145 149 162 0 1.332 1.317 1.318 3.967 0.000 0.191
151 2 1 158 0 0.873 1.075 0.000 0.366
152 2 1 158 0 0.897 1.056 0.000 0.386
153 2 1 160 0 0.905 1.051 0.000 0.379
154 2 2 167 160 0 0.267 0.838 1.105 0.000 0.385
155 2 2 168 162 0 0.216 0.868 1.083 0.000 0.377
156 2 1 162 0 0.881 1.069 0.000 0.386
158 4 3 151 152 146 0 0.873 0.897 1.300 3.070 0.966 -0.469
159 4 3 147 165 166 0 1.083 1.211 1.214 3.508 0.160 0.371
160 4 3 148 153 154 0 1.324 0.905 0.838 3.068 0.968 -0.443
161 4 3 149 167 168 0 1.143 1.171 1.190 3.504 0.165 0.341
162 4 3 150 155 156 0 1.318 0.868 0.881 3.067 0.969 -0.438
165 3 1 159 0 1.211 1.378 2.000 -0.375
166 3 1 159 0 1.214 1.368 2.000 -0.399
167 3 2 154 161 0 0.267 1.171 1.446 2.000 -0.388
168 3 2 155 161 0 0.216 1.190 1.413 2.000 -0.411
169 1 3 174 170 181 0 1.332 1.324 1.109 3.767 0.000 -0.073
170 1 3 169 171 182 0 1.324 1.345 1.300 3.969 0.000 0.193
171 1 3 170 172 183 0 1.345 1.336 1.083 3.767 0.000 -0.060
172 1 3 171 173 184 0 1.336 1.306 1.324 3.967 0.000 0.196
173 1 3 172 174 185 0 1.306 1.317 1.143 3.769 0.000 -0.063
174 1 3 169 173 186 0 1.332 1.317 1.318 3.967 0.000 0.191
175 2 1 182 0 0.873 1.075 0.000 0.366
176 2 1 182 0 0.897 1.056 0.000 0.386
177 2 1 184 0 0.905 1.051 0.000 0.379
178 2 2 191 184 0 0.267 0.838 1.105 0.000 0.385
179 2 2 186 192 0 0.868 0.216 1.083 0.000 0.377
180 2 1 186 0 0.881 1.069 0.000 0.386
181 4 3 169 187 188 0 1.109 1.197 1.198 3.504 0.165 0.344
182 4 3 170 175 176 0 1.300 0.873 0.897 3.070 0.966 -0.469
183 4 3 171 189 190 0 1.083 1.211 1.214 3.508 0.160 0.371
184 4 3 172 177 178 0 1.324 0.905 0.838 3.068 0.968 -0.443
185 4 3 173 191 192 0 1.143 1.171 1.190 3.504 0.165 0.341
186 4 3 174 179 180 0 1.318 0.868 0.881 3.067 0.969 -0.438
187 3 1 181 0 1.197 1.393 2.000 -0.381
188 3 1 181 0 1.198 1.407 2.000 -0.413
189 3 1 183 0 1.211 1.378 2.000 -0.375
190 3 1 183 0 1.214 1.368 2.000 -0.399
191 3 2 178 185 0 0.267 1.171 1.446 2.000 -0.388
192 3 2 179 185 0 0.216 1.190 1.413 2.000 -0.411
193 1 3 194 198 205 0 1.324 1.332 1.109 3.767 0.000 -0.073
194 1 3 193 195 206 0 1.324 1.345 1.300 3.969 0.000 0.193
195 1 3 194 196 207 0 1.345 1.336 1.083 3.767 0.000 -0.060
196 1 3 195 197 208 0 1.336 1.306 1.324 3.967 0.000 0.196
197 1 3 196 198 209 0 1.306 1.317 1.143 3.769 0.000 -0.063
198 1 3 193 197 210 0 1.332 1.317 1.318 3.967 0.000 0.191
199 2 1 206 0 0.873 1.075 0.000 0.366
200 2 1 206 0 0.897 1.056 0.000 0.386
201 2 1 208 0 0.905 1.051 0.000 0.379
202 2 2 208 215 0 0.838 0.267 1.105 0.000 0.385
203 2 2 210 216 0 0.868 0.216 1.083 0.000 0.377
204 2 1 210 0 0.881 1.069 0.000 0.386
205 4 3 212 193 211 0 1.198 1.109 1.197 3.504 0.165 0.344
206 4 3 199 200 194 0 0.873 0.897 1.300 3.070 0.966 -0.469
207 4 3 195 213 214 0 1.083 1.211 1.214 3.508 0.160 0.371
208 4 3 196 201 202 0 1.324 0.905 0.838 3.068 0.968 -0.443
209 4 3 197 215 216 0 1.143 1.171 1.190 3.504 0.165 0.341
210 4 3 198 203 204 0 1.318 0.868 0.881 3.067 0.969 -0.438
211 3 1 205 0 1.197 1.393 2.000 -0.381
212 3 1 205 0 1.198 1.407 2.000 -0.413
213 3 1 207 0 1.211 1.378 2.000 -0.375
214 3 1 207 0 1.214 1.368 2.000 -0.399
215 3 2 202 209 0 0.267 1.171 1.446 2.000 -0.388
216 3 2 203 209 0 0.216 1.190 1.413 2.000 -0.411
217 1 3 218 222 229 0 1.324 1.332 1.109 3.767 0.000 -0.073
218 1 3 217 219 230 0 1.324 1.345 1.300 3.969 0.000 0.193
219 1 3 218 220 231 0 1.345 1.336 1.083 3.767 0.000 -0.060
220 1 3 219 221 232 0 1.336 1.306 1.324 3.967 0.000 0.196
221 1 3 220 222 233 0 1.306 1.317 1.143 3.769 0.000 -0.063
222 1 3 217 221 234 0 1.332 1.317 1.318 3.967 0.000 0.191
223 2 1 230 0 0.873 1.075 0.000 0.366
224 2 1 230 0 0.897 1.056 0.000 0.386
225 2 1 232 0 0.905 1.051 0.000 0.379
226 2 2 239 232 0 0.267 0.838 1.105 0.000 0.385
227 2 2 234 240 0 0.868 0.216 1.083 0.000 0.377
228 2 1 234 0 0.881 1.069 0.000 0.386
229 4 3 217 235 236 0 1.109 1.197 1.198 3.504 0.165 0.344
230 4 3 218 223 224 0 1.300 0.873 0.897 3.070 0.966 -0.469
231 4 3 219 237 238 0 1.083 1.211 1.214 3.508 0.160 0.371
232 4 3 225 226 220 0 0.905 0.838 1.324 3.068 0.968 -0.443
233 4 3 221 239 240 0 1.143 1.171 1.190 3.504 0.165 0.341
234 4 3 222 227 228 0 1.318 0.868 0.881 3.067 0.969 -0.438
235 3 1 229 0 1.197 1.393 2.000 -0.381
236 3 1 229 0 1.198 1.407 2.000 -0.413
237 3 1 231 0 1.211 1.378 2.000 -0.375
238 3 1 231 0 1.214 1.368 2.000 -0.399
239 3 2 233 226 0 1.171 0.267 1.446 2.000 -0.388
240 3 2 227 233 0 0.216 1.190 1.413 2.000 -0.411
241 1 3 242 246 253 0 1.324 1.332 1.109 3.767 0.000 -0.073
242 1 3 241 243 254 0 1.324 1.345 1.300 3.969 0.000 0.193
243 1 3 242 244 255 0 1.345 1.336 1.083 3.767 0.000 -0.060
244 1 3 243 245 256 0 1.336 1.306 1.324 3.967 0.000 0.196
245 1 3 244 246 257 0 1.306 1.317 1.143 3.769 0.000 -0.063
246 1 3 241 245 258 0 1.332 1.317 1.318 3.967 0.000 0.191
247 2 1 254 0 0.873 1.075 0.000 0.366
248 2 1 254 0 0.897 1.056 0.000 0.386
249 2 1 256 0 0.905 1.051 0.000 0.379
250 2 2 256 263 0 0.838 0.267 1.105 0.000 0.385
251 2 2 258 264 0 0.868 0.216 1.083 0.000 0.377
252 2 1 258 0 0.881 1.069 0.000 0.386
254 4 3 247 248 242 0 0.873 0.897 1.300 3.070 0.966 -0.469
255 4 3 243 261 262 0 1.083 1.211 1.214 3.508 0.160 0.371
256 4 3 244 249 250 0 1.324 0.905 0.838 3.068 0.968 -0.443
257 4 3 245 263 264 0 1.143 1.171 1.190 3.504 0.165 0.341
258 4 3 246 251 252 0 1.318 0.868 0.881 3.067 0.969 -0.438
261 3 1 255 0 1.211 1.378 2.000 -0.375
262 3 1 255 0 1.214 1.368 2.000 -0.399
263 3 2 250 257 0 0.267 1.171 1.446 2.000 -0.388
264 3 2 251 257 0 0.216 1.190 1.413 2.000 -0.411
265 1 3 266 270 277 0 1.324 1.332 1.109 3.767 0.000 -0.073
266 1 3 265 267 278 0 1.324 1.345 1.300 3.969 0.000 0.193
267 1 3 266 268 279 0 1.345 1.336 1.083 3.767 0.000 -0.060
268 1 3 267 269 280 0 1.336 1.306 1.324 3.967 0.000 0.196
269 1 3 268 270 281 0 1.306 1.317 1.143 3.769 0.000 -0.063
270 1 3 265 269 282 0 1.332 1.317 1.318 3.967 0.000 0.191
271 2 1 278 0 0.873 1.075 0.000 0.366
272 2 1 278 0 0.897 1.056 0.000 0.386
273 2 1 280 0 0.905 1.051 0.000 0.379
274 2 2 287 280 0 0.267 0.838 1.105 0.000 0.385
275 2 2 282 288 0 0.868 0.216 1.083 0.000 0.377
276 2 1 282 0 0.881 1.069 0.000 0.386
277 4 3 265 283 284 0 1.109 1.197 1.198 3.504 0.165 0.344
278 4 3 266 271 272 0 1.300 0.873 0.897 3.070 0.966 -0.469
279 4 3 267 285 286 0 1.083 1.211 1.214 3.508 0.160 0.371
280 4 3 273 274 268 0 0.905 0.838 1.324 3.068 0.968 -0.443
281 4 3 269 287 288 0 1.143 1.171 1.190 3.504 0.165 0.341
282 4 3 270 275 276 0 1.318 0.868 0.881 3.067 0.969 -0.438
283 3 1 277 0 1.197 1.393 2.000 -0.381
284 3 1 277 0 1.198 1.407 2.000 -0.413
285 3 1 279 0 1.211 1.378 2.000 -0.375
286 3 1 279 0 1.214 1.368 2.000 -0.399
287 3 2 281 274 0 1.171 0.267 1.446 2.000 -0.388
288 3 2 275 281 0 0.216 1.190 1.413 2.000 -0.411
289 1 3 290 294 301 0 1.324 1.332 1.109 3.767 0.000 -0.073
290 1 3 289 291 302 0 1.324 1.345 1.300 3.969 0.000 0.193
291 1 3 290 303 292 0 1.345 1.083 1.337 3.767 0.000 -0.060
292 1 3 291 293 304 0 1.337 1.306 1.324 3.967 0.000 0.196
293 1 3 292 294 305 0 1.306 1.317 1.143 3.769 0.000 -0.063
294 1 3 289 293 306 0 1.332 1.317 1.318 3.967 0.000 0.191
295 2 1 302 0 0.873 1.075 0.000 0.366
296 2 1 302 0 0.897 1.056 0.000 0.386
297 2 1 304 0 0.905 1.051 0.000 0.379
298 2 2 311 304 0 0.267 0.838 1.105 0.000 0.385
299 2 2 312 306 0 0.216 0.868 1.083 0.000 0.377
300 2 1 306 0 0.881 1.069 0.000 0.386
301 4 3 289 308 307 0 1.109 1.198 1.197 3.504 0.165 0.344
302 4 3 290 295 296 0 1.300 0.873 0.897 3.070 0.966 -0.469
303 4 3 291 309 310 0 1.083 1.211 1.214 3.508 0.160 0.371
304 4 3 292 297 298 0 1.324 0.905 0.838 3.068 0.968 -0.443
305 4 3 293 311 312 0 1.143 1.171 1.190 3.504 0.165 0.341
306 4 3 294 299 300 0 1.318 0.868 0.881 3.067 0.969 -0.438
307 3 1 301 0 1.197 1.393 2.000 -0.381
308 3 1 301 0 1.198 1.407 2.000 -0.413
309 3 1 303 0 1.211 1.378 2.000 -0.375
310 3 1 303 0 1.214 1.368 2.000 -0.399
311 3 2 298 305 0 0.267 1.171 1.446 2.000 -0.388
312 3 2 299 305 0 0.216 1.190 1.413 2.000 -0.411
313 1 3 314 318 325 0 1.324 1.332 1.109 3.767 0.000 -0.073
314 1 3 313 315 326 0 1.324 1.345 1.300 3.969 0.000 0.193
315 1 3 314 316 327 0 1.345 1.336 1.083 3.767 0.000 -0.060
316 1 3 315 317 328 0 1.336 1.306 1.324 3.967 0.000 0.196
317 1 3 316 318 329 0 1.306 1.317 1.143 3.769 0.000 -0.063
318 1 3 313 317 330 0 1.332 1.317 1.318 3.967 0.000 0.191
319 2 1 326 0 0.873 1.075 0.000 0.366
320 2 1 326 0 0.897 1.056 0.000 0.386
321 2 1 328 0 0.905 1.051 0.000 0.379
322 2 2 335 328 0 0.267 0.838 1.105 0.000 0.385
323 2 2 330 336 0 0.868 0.216 1.083 0.000 0.377
324 2 1 330 0 0.881 1.069 0.000 0.386
325 4 3 313 331 332 0 1.109 1.197 1.198 3.504 0.165 0.344
326 4 3 314 320 319 0 1.300 0.897 0.873 3.070 0.966 -0.469
327 4 3 315 333 334 0 1.083 1.211 1.214 3.508 0.160 0.371
328 4 3 321 322 316 0 0.905 0.838 1.324 3.068 0.968 -0.443
329 4 3 317 335 336 0 1.143 1.171 1.190 3.504 0.165 0.341
330 4 3 318 323 324 0 1.318 0.868 0.881 3.067 0.969 -0.438
331 3 1 325 0 1.197 1.393 2.000 -0.381
332 3 1 325 0 1.198 1.407 2.000 -0.413
333 3 1 327 0 1.211 1.378 2.000 -0.375
334 3 1 327 0 1.214 1.368 2.000 -0.399
335 3 2 329 322 0 1.171 0.267 1.446 2.000 -0.388
336 3 2 323 329 0 0.216 1.190 1.413 2.000 -0.411
337 1 3 338 342 349 0 1.324 1.332 1.109 3.767 0.000 -0.073
338 1 3 337 339 350 0 1.324 1.345 1.300 3.969 0.000 0.193
339 1 3 338 351 340 0 1.345 1.083 1.337 3.767 0.000 -0.060
340 1 3 339 341 352 0 1.337 1.306 1.324 3.967 0.000 0.196
341 1 3 340 342 353 0 1.306 1.317 1.143 3.769 0.000 -0.063
342 1 3 337 341 354 0 1.332 1.317 1.318 3.967 0.000 0.191
343 2 1 350 0 0.873 1.075 0.000 0.366
344 2 1 350 0 0.897 1.056 0.000 0.386
345 2 1 352 0 0.905 1.051 0.000 0.379
346 2 2 352 359 0 0.838 0.267 1.105 0.000 0.385
347 2 2 360 354 0 0.216 0.868 1.083 0.000 0.377
348 2 1 354 0 0.881 1.069 0.000 0.386
350 4 3 338 343 344 0 1.300 0.873 0.897 3.070 0.966 -0.469
351 4 3 339 357 358 0 1.083 1.211 1.214 3.508 0.160 0.371
352 4 3 340 345 346 0 1.324 0.905 0.838 3.068 0.968 -0.443
353 4 3 341 360 359 0 1.143 1.190 1.171 3.504 0.165 0.341
354 4 3 342 347 348 0 1.318 0.868 0.881 3.067 0.969 -0.438
357 3 1 351 0 1.211 1.378 2.000 -0.375
358 3 1 351 0 1.214 1.368 2.000 -0.399
359 3 2 346 353 0 0.267 1.171 1.446 2.000 -0.388
360 3 2 347 353 0 0.216 1.190 1.413 2.000 -0.411
361 1 3 362 366 373 0 1.324 1.332 1.109 3.767 0.000 -0.073
362 1 3 361 363 374 0 1.324 1.345 1.300 3.969 0.000 0.193
363 1 3 362 364 375 0 1.345 1.336 1.083 3.767 0.000 -0.060
364 1 3 363 365 376 0 1.336 1.306 1.324 3.967 0.000 0.196
365 1 3 364 366 377 0 1.306 1.317 1.143 3.769 0.000 -0.063
366 1 3 361 365 378 0 1.332 1.317 1.318 3.967 0.000 0.191
367 2 1 374 0 0.873 1.075 0.000 0.366
368 2 1 374 0 0.897 1.056 0.000 0.386
369 2 1 376 0 0.905 1.051 0.000 0.379
370 2 2 383 376 0 0.267 0.838 1.105 0.000 0.385
371 2 2 378 384 0 0.868 0.216 1.083 0.000 0.377
372 2 1 378 0 0.881 1.069 0.000 0.386
373 4 3 361 379 380 0 1.109 1.197 1.198 3.504 0.165 0.344
374 4 3 362 368 367 0 1.300 0.897 0.873 3.070 0.966 -0.469
375 4 3 363 381 382 0 1.083 1.211 1.214 3.508 0.160 0.371
376 4 3 369 370 364 0 0.905 0.838 1.324 3.068 0.968 -0.443
377 4 3 365 383 384 0 1.143 1.171 1.190 3.504 0.165 0.341
378 4 3 366 371 372 0 1.318 0.868 0.881 3.067 0.969 -0.438
379 3 1 373 0 1.197 1.393 2.000 -0.381
380 3 1 373 0 1.198 1.407 2.000 -0.413
381 3 1 375 0 1.211 1.378 2.000 -0.375
382 3 1 375 0 1.214 1.368 2.000 -0.399
383 3 2 377 370 0 1.171 0.267 1.446 2.000 -0.388
384 3 2 371 377 0 0.216 1.190 1.413 2.000 -0.411
61 4 3 49 68 67 0 1.109 1.198 1.197 3.504 0.165 0.344
67 3 1 61 0 1.197 1.393 2.000 -0.381
68 3 1 61 0 1.198 1.407 2.000 -0.413
157 4 3 164 145 163 0 1.198 1.109 1.197 3.504 0.165 0.344
163 3 1 157 0 1.197 1.393 2.000 -0.381
164 3 1 157 0 1.198 1.407 2.000 -0.413
253 4 3 260 241 259 0 1.198 1.109 1.197 3.504 0.165 0.344
259 3 1 253 0 1.197 1.393 2.000 -0.381
260 3 1 253 0 1.198 1.407 2.000 -0.413
349 4 3 337 356 355 0 1.109 1.198 1.197 3.504 0.165 0.344
355 3 1 349 0 1.197 1.393 2.000 -0.381
356 3 1 349 0 1.198 1.407 2.000 -0.413
#
# Timestep 25
#
# Number of particles 384
#
# Max.number of bonds per atom 3 with coarse bond order cutoff 0.300
# Particle connection table and bond orders
# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q
1 1 3 2 6 13 0 1.321 1.328 1.129 3.783 0.000 -0.075
2 1 3 1 3 14 0 1.321 1.341 1.325 3.987 0.000 0.190
3 1 3 2 4 15 0 1.341 1.333 1.103 3.783 0.000 -0.063
4 1 3 3 5 16 0 1.333 1.303 1.350 3.985 0.000 0.194
5 1 3 4 6 17 0 1.303 1.313 1.161 3.784 0.000 -0.066
6 1 3 1 5 18 0 1.328 1.313 1.344 3.985 0.000 0.188
7 2 2 14 20 0 0.855 0.269 1.123 0.000 0.366
8 2 2 14 21 0 0.878 0.236 1.114 0.000 0.387
9 2 2 16 22 0 0.885 0.232 1.116 0.000 0.380
10 2 2 16 23 0 0.827 0.291 1.118 0.000 0.385
11 2 2 18 24 0 0.852 0.273 1.124 0.000 0.377
12 2 2 18 19 0 0.862 0.262 1.125 0.000 0.387
13 4 3 1 20 19 0 1.129 1.232 1.231 3.591 0.083 0.362
14 4 3 2 7 8 0 1.325 0.855 0.878 3.058 0.977 -0.457
15 4 3 3 21 22 0 1.103 1.245 1.247 3.595 0.081 0.390
16 4 3 4 9 10 0 1.350 0.885 0.827 3.061 0.974 -0.433
17 4 3 5 23 24 0 1.161 1.206 1.224 3.591 0.084 0.359
18 4 3 6 11 12 0 1.344 0.852 0.862 3.058 0.977 -0.427
19 3 2 12 13 0 0.262 1.231 1.504 2.000 -0.395
20 3 2 7 13 0 0.269 1.232 1.511 2.000 -0.426
21 3 2 8 15 0 0.236 1.245 1.491 2.000 -0.389
22 3 2 9 15 0 0.232 1.247 1.489 2.000 -0.415
23 3 2 10 17 0 0.291 1.206 1.508 2.000 -0.397
24 3 2 11 17 0 0.273 1.224 1.507 2.000 -0.422
25 1 3 30 26 37 0 1.328 1.321 1.129 3.783 0.000 -0.075
26 1 3 25 27 38 0 1.321 1.341 1.325 3.987 0.000 0.190
27 1 3 26 28 39 0 1.341 1.333 1.103 3.783 0.000 -0.063
28 1 3 27 29 40 0 1.333 1.303 1.350 3.985 0.000 0.194
29 1 3 28 30 41 0 1.303 1.313 1.161 3.784 0.000 -0.066
30 1 3 25 29 42 0 1.328 1.313 1.344 3.985 0.000 0.188
31 2 2 44 38 0 0.269 0.855 1.123 0.000 0.366
32 2 2 38 45 0 0.878 0.236 1.114 0.000 0.387
33 2 2 40 46 0 0.885 0.232 1.116 0.000 0.380
34 2 2 47 40 0 0.291 0.827 1.118 0.000 0.385
35 2 2 42 48 0 0.852 0.273 1.124 0.000 0.377
36 2 2 42 43 0 0.862 0.262 1.125 0.000 0.387
37 4 3 25 43 44 0 1.129 1.231 1.232 3.591 0.083 0.362
38 4 3 26 32 31 0 1.325 0.878 0.855 3.058 0.977 -0.457
39 4 3 27 45 46 0 1.103 1.245 1.247 3.595 0.081 0.390
40 4 3 28 33 34 0 1.350 0.885 0.827 3.061 0.974 -0.433
41 4 3 29 47 48 0 1.161 1.206 1.224 3.591 0.084 0.359
42 4 3 30 35 36 0 1.344 0.852 0.862 3.058 0.977 -0.427
43 3 2 36 37 0 0.262 1.231 1.504 2.000 -0.395
44 3 2 31 37 0 0.269 1.232 1.511 2.000 -0.426
45 3 2 32 39 0 0.236 1.245 1.491 2.000 -0.389
46 3 2 33 39 0 0.232 1.247 1.489 2.000 -0.415
47 3 2 34 41 0 0.291 1.206 1.508 2.000 -0.397
48 3 2 35 41 0 0.273 1.224 1.507 2.000 -0.422
49 1 3 50 54 61 0 1.321 1.328 1.129 3.783 0.000 -0.075
50 1 3 49 51 62 0 1.321 1.341 1.325 3.987 0.000 0.190
51 1 3 50 52 63 0 1.341 1.333 1.103 3.783 0.000 -0.063
52 1 3 51 53 64 0 1.333 1.303 1.350 3.985 0.000 0.194
53 1 3 52 54 65 0 1.303 1.313 1.161 3.784 0.000 -0.066
54 1 3 49 53 66 0 1.328 1.313 1.344 3.985 0.000 0.188
55 2 2 62 68 0 0.855 0.269 1.123 0.000 0.366
56 2 2 62 69 0 0.878 0.236 1.114 0.000 0.387
57 2 2 64 70 0 0.885 0.232 1.116 0.000 0.380
58 2 2 64 71 0 0.827 0.291 1.118 0.000 0.385
59 2 2 66 72 0 0.852 0.273 1.124 0.000 0.377
60 2 2 66 67 0 0.862 0.262 1.125 0.000 0.387
62 4 3 50 55 56 0 1.325 0.855 0.878 3.058 0.977 -0.457
63 4 3 51 69 70 0 1.103 1.245 1.247 3.595 0.081 0.390
64 4 3 52 57 58 0 1.350 0.885 0.827 3.061 0.974 -0.433
65 4 3 53 71 72 0 1.161 1.206 1.224 3.591 0.084 0.359
66 4 3 54 59 60 0 1.344 0.852 0.862 3.058 0.977 -0.427
69 3 2 56 63 0 0.236 1.245 1.491 2.000 -0.389
70 3 2 57 63 0 0.232 1.247 1.489 2.000 -0.415
71 3 2 58 65 0 0.291 1.206 1.508 2.000 -0.397
72 3 2 59 65 0 0.273 1.224 1.507 2.000 -0.422
73 1 3 78 74 85 0 1.328 1.321 1.129 3.783 0.000 -0.075
74 1 3 73 75 86 0 1.321 1.341 1.325 3.987 0.000 0.190
75 1 3 74 76 87 0 1.341 1.333 1.103 3.783 0.000 -0.063
76 1 3 75 77 88 0 1.333 1.303 1.350 3.985 0.000 0.194
77 1 3 76 78 89 0 1.303 1.313 1.161 3.784 0.000 -0.066
78 1 3 73 77 90 0 1.328 1.313 1.344 3.985 0.000 0.188
79 2 2 92 86 0 0.269 0.855 1.123 0.000 0.366
80 2 2 86 93 0 0.878 0.236 1.114 0.000 0.387
81 2 2 88 94 0 0.885 0.232 1.116 0.000 0.380
82 2 2 95 88 0 0.291 0.827 1.118 0.000 0.385
83 2 2 90 96 0 0.852 0.273 1.124 0.000 0.377
84 2 2 90 91 0 0.862 0.262 1.125 0.000 0.387
85 4 3 73 91 92 0 1.129 1.231 1.232 3.591 0.083 0.362
86 4 3 74 80 79 0 1.325 0.878 0.855 3.058 0.977 -0.457
87 4 3 75 93 94 0 1.103 1.245 1.247 3.595 0.081 0.390
88 4 3 76 81 82 0 1.350 0.885 0.827 3.061 0.974 -0.433
89 4 3 77 95 96 0 1.161 1.206 1.224 3.591 0.084 0.359
90 4 3 78 83 84 0 1.344 0.852 0.862 3.058 0.977 -0.427
91 3 2 84 85 0 0.262 1.231 1.504 2.000 -0.395
92 3 2 79 85 0 0.269 1.232 1.511 2.000 -0.426
93 3 2 80 87 0 0.236 1.245 1.491 2.000 -0.389
94 3 2 81 87 0 0.232 1.247 1.489 2.000 -0.415
95 3 2 82 89 0 0.291 1.206 1.508 2.000 -0.397
96 3 2 83 89 0 0.273 1.224 1.507 2.000 -0.422
97 1 3 109 98 102 0 1.129 1.321 1.328 3.783 0.000 -0.075
98 1 3 99 97 110 0 1.341 1.321 1.325 3.987 0.000 0.190
99 1 3 98 100 111 0 1.341 1.333 1.103 3.783 0.000 -0.063
100 1 3 99 101 112 0 1.333 1.303 1.350 3.985 0.000 0.194
101 1 3 100 113 102 0 1.303 1.161 1.313 3.784 0.000 -0.066
102 1 3 101 114 97 0 1.313 1.344 1.328 3.985 0.000 0.188
103 2 2 110 116 0 0.855 0.269 1.123 0.000 0.366
104 2 2 110 117 0 0.878 0.236 1.114 0.000 0.387
105 2 2 112 118 0 0.885 0.232 1.116 0.000 0.380
106 2 2 119 112 0 0.291 0.827 1.118 0.000 0.385
107 2 2 114 120 0 0.852 0.273 1.124 0.000 0.377
108 2 2 114 115 0 0.862 0.262 1.125 0.000 0.387
109 4 3 97 116 115 0 1.129 1.232 1.231 3.591 0.083 0.362
110 4 3 103 104 98 0 0.855 0.878 1.325 3.058 0.977 -0.457
111 4 3 99 117 118 0 1.103 1.245 1.247 3.595 0.081 0.390
112 4 3 100 105 106 0 1.350 0.885 0.827 3.061 0.974 -0.433
113 4 3 101 119 120 0 1.161 1.206 1.224 3.591 0.084 0.359
114 4 3 102 107 108 0 1.344 0.852 0.862 3.058 0.977 -0.427
115 3 2 109 108 0 1.231 0.262 1.504 2.000 -0.395
116 3 2 103 109 0 0.269 1.232 1.511 2.000 -0.426
117 3 2 111 104 0 1.245 0.236 1.491 2.000 -0.389
118 3 2 105 111 0 0.232 1.247 1.489 2.000 -0.415
119 3 2 106 113 0 0.291 1.206 1.508 2.000 -0.397
120 3 2 107 113 0 0.273 1.224 1.507 2.000 -0.422
121 1 3 126 122 133 0 1.328 1.321 1.129 3.783 0.000 -0.075
122 1 3 121 123 134 0 1.321 1.341 1.325 3.987 0.000 0.190
123 1 3 122 124 135 0 1.341 1.333 1.103 3.783 0.000 -0.063
124 1 3 123 125 136 0 1.333 1.303 1.350 3.985 0.000 0.194
125 1 3 124 126 137 0 1.303 1.313 1.161 3.784 0.000 -0.066
126 1 3 121 125 138 0 1.328 1.313 1.344 3.985 0.000 0.188
127 2 2 134 140 0 0.855 0.269 1.123 0.000 0.366
128 2 2 134 141 0 0.878 0.236 1.114 0.000 0.387
129 2 2 136 142 0 0.885 0.232 1.116 0.000 0.380
130 2 2 143 136 0 0.291 0.827 1.118 0.000 0.385
131 2 2 138 144 0 0.852 0.273 1.124 0.000 0.377
132 2 2 138 139 0 0.862 0.262 1.125 0.000 0.387
133 4 3 121 139 140 0 1.129 1.231 1.232 3.591 0.083 0.362
134 4 3 122 127 128 0 1.325 0.855 0.878 3.058 0.977 -0.457
135 4 3 123 141 142 0 1.103 1.245 1.247 3.595 0.081 0.390
136 4 3 124 129 130 0 1.350 0.885 0.827 3.061 0.974 -0.433
137 4 3 125 143 144 0 1.161 1.206 1.224 3.591 0.084 0.359
138 4 3 126 131 132 0 1.344 0.852 0.862 3.058 0.977 -0.427
139 3 2 132 133 0 0.262 1.231 1.504 2.000 -0.395
140 3 2 127 133 0 0.269 1.232 1.511 2.000 -0.426
141 3 2 128 135 0 0.236 1.245 1.491 2.000 -0.389
142 3 2 129 135 0 0.232 1.247 1.489 2.000 -0.415
143 3 2 130 137 0 0.291 1.206 1.508 2.000 -0.397
144 3 2 131 137 0 0.273 1.224 1.507 2.000 -0.422
145 1 3 157 146 150 0 1.129 1.321 1.328 3.783 0.000 -0.075
146 1 3 147 145 158 0 1.341 1.321 1.325 3.987 0.000 0.190
147 1 3 146 148 159 0 1.341 1.333 1.103 3.783 0.000 -0.063
148 1 3 147 149 160 0 1.333 1.303 1.350 3.985 0.000 0.194
149 1 3 148 161 150 0 1.303 1.161 1.313 3.784 0.000 -0.066
150 1 3 149 162 145 0 1.313 1.344 1.328 3.985 0.000 0.188
151 2 2 158 164 0 0.855 0.269 1.123 0.000 0.366
152 2 2 158 165 0 0.878 0.236 1.114 0.000 0.387
153 2 2 160 166 0 0.885 0.232 1.116 0.000 0.380
154 2 2 167 160 0 0.291 0.827 1.118 0.000 0.385
155 2 2 168 162 0 0.273 0.852 1.124 0.000 0.377
156 2 2 162 163 0 0.862 0.262 1.125 0.000 0.387
158 4 3 151 152 146 0 0.855 0.878 1.325 3.058 0.977 -0.457
159 4 3 147 165 166 0 1.103 1.245 1.247 3.595 0.081 0.390
160 4 3 148 153 154 0 1.350 0.885 0.827 3.061 0.974 -0.433
161 4 3 149 167 168 0 1.161 1.206 1.224 3.591 0.084 0.359
162 4 3 150 155 156 0 1.344 0.852 0.862 3.058 0.977 -0.427
165 3 2 159 152 0 1.245 0.236 1.491 2.000 -0.389
166 3 2 153 159 0 0.232 1.247 1.489 2.000 -0.415
167 3 2 154 161 0 0.291 1.206 1.508 2.000 -0.397
168 3 2 155 161 0 0.273 1.224 1.507 2.000 -0.422
169 1 3 174 170 181 0 1.328 1.321 1.129 3.783 0.000 -0.075
170 1 3 169 171 182 0 1.321 1.341 1.325 3.987 0.000 0.190
171 1 3 170 172 183 0 1.341 1.333 1.103 3.783 0.000 -0.063
172 1 3 171 173 184 0 1.333 1.303 1.350 3.985 0.000 0.194
173 1 3 172 174 185 0 1.303 1.313 1.161 3.784 0.000 -0.066
174 1 3 169 173 186 0 1.328 1.313 1.344 3.985 0.000 0.188
175 2 2 182 188 0 0.855 0.269 1.123 0.000 0.366
176 2 2 182 189 0 0.878 0.236 1.114 0.000 0.387
177 2 2 184 190 0 0.885 0.232 1.116 0.000 0.380
178 2 2 191 184 0 0.291 0.827 1.118 0.000 0.385
179 2 2 186 192 0 0.852 0.273 1.124 0.000 0.377
180 2 2 186 187 0 0.862 0.262 1.125 0.000 0.387
181 4 3 169 187 188 0 1.129 1.231 1.232 3.591 0.083 0.362
182 4 3 170 175 176 0 1.325 0.855 0.878 3.058 0.977 -0.457
183 4 3 171 189 190 0 1.103 1.245 1.247 3.595 0.081 0.390
184 4 3 172 177 178 0 1.350 0.885 0.827 3.061 0.974 -0.433
185 4 3 173 191 192 0 1.161 1.206 1.224 3.591 0.084 0.359
186 4 3 174 179 180 0 1.344 0.852 0.862 3.058 0.977 -0.427
187 3 2 180 181 0 0.262 1.231 1.504 2.000 -0.395
188 3 2 175 181 0 0.269 1.232 1.511 2.000 -0.426
189 3 2 176 183 0 0.236 1.245 1.491 2.000 -0.389
190 3 2 177 183 0 0.232 1.247 1.489 2.000 -0.415
191 3 2 178 185 0 0.291 1.206 1.508 2.000 -0.397
192 3 2 179 185 0 0.273 1.224 1.507 2.000 -0.422
193 1 3 205 194 198 0 1.129 1.321 1.328 3.783 0.000 -0.075
194 1 3 195 193 206 0 1.341 1.321 1.325 3.987 0.000 0.190
195 1 3 194 196 207 0 1.341 1.333 1.103 3.783 0.000 -0.063
196 1 3 195 197 208 0 1.333 1.303 1.350 3.985 0.000 0.194
197 1 3 196 198 209 0 1.303 1.313 1.161 3.784 0.000 -0.066
198 1 3 197 193 210 0 1.313 1.328 1.344 3.985 0.000 0.188
199 2 2 206 212 0 0.855 0.269 1.123 0.000 0.366
200 2 2 206 213 0 0.878 0.236 1.114 0.000 0.387
201 2 2 214 208 0 0.232 0.885 1.116 0.000 0.380
202 2 2 208 215 0 0.827 0.291 1.118 0.000 0.385
203 2 2 210 216 0 0.852 0.273 1.124 0.000 0.377
204 2 2 210 211 0 0.862 0.262 1.125 0.000 0.387
205 4 3 193 212 211 0 1.129 1.232 1.231 3.591 0.083 0.362
206 4 3 199 200 194 0 0.855 0.878 1.325 3.058 0.977 -0.457
207 4 3 195 213 214 0 1.103 1.245 1.247 3.595 0.081 0.390
208 4 3 196 201 202 0 1.350 0.885 0.827 3.061 0.974 -0.433
209 4 3 197 215 216 0 1.161 1.206 1.224 3.591 0.084 0.359
210 4 3 198 203 204 0 1.344 0.852 0.862 3.058 0.977 -0.427
211 3 2 205 204 0 1.231 0.262 1.504 2.000 -0.395
212 3 2 199 205 0 0.269 1.232 1.511 2.000 -0.426
213 3 2 207 200 0 1.245 0.236 1.491 2.000 -0.389
214 3 2 201 207 0 0.232 1.247 1.489 2.000 -0.415
215 3 2 202 209 0 0.291 1.206 1.508 2.000 -0.397
216 3 2 203 209 0 0.273 1.224 1.507 2.000 -0.422
217 1 3 218 222 229 0 1.321 1.328 1.129 3.783 0.000 -0.075
218 1 3 217 219 230 0 1.321 1.341 1.325 3.987 0.000 0.190
219 1 3 218 220 231 0 1.341 1.333 1.103 3.783 0.000 -0.063
220 1 3 219 221 232 0 1.333 1.303 1.350 3.985 0.000 0.194
221 1 3 220 222 233 0 1.303 1.313 1.161 3.784 0.000 -0.066
222 1 3 217 221 234 0 1.328 1.313 1.344 3.985 0.000 0.188
223 2 2 230 236 0 0.855 0.269 1.123 0.000 0.366
224 2 2 230 237 0 0.878 0.236 1.114 0.000 0.387
225 2 2 232 238 0 0.885 0.232 1.116 0.000 0.380
226 2 2 239 232 0 0.291 0.827 1.118 0.000 0.385
227 2 2 234 240 0 0.852 0.273 1.124 0.000 0.377
228 2 2 234 235 0 0.862 0.262 1.125 0.000 0.387
229 4 3 217 235 236 0 1.129 1.231 1.232 3.591 0.083 0.362
230 4 3 218 223 224 0 1.325 0.855 0.878 3.058 0.977 -0.457
231 4 3 219 237 238 0 1.103 1.245 1.247 3.595 0.081 0.390
232 4 3 225 226 220 0 0.885 0.827 1.350 3.061 0.974 -0.433
233 4 3 221 239 240 0 1.161 1.206 1.224 3.591 0.084 0.359
234 4 3 222 227 228 0 1.344 0.852 0.862 3.058 0.977 -0.427
235 3 2 228 229 0 0.262 1.231 1.504 2.000 -0.395
236 3 2 223 229 0 0.269 1.232 1.511 2.000 -0.426
237 3 2 231 224 0 1.245 0.236 1.491 2.000 -0.389
238 3 2 225 231 0 0.232 1.247 1.489 2.000 -0.415
239 3 2 233 226 0 1.206 0.291 1.508 2.000 -0.397
240 3 2 227 233 0 0.273 1.224 1.507 2.000 -0.422
241 1 3 253 242 246 0 1.129 1.321 1.328 3.783 0.000 -0.075
242 1 3 243 241 254 0 1.341 1.321 1.325 3.987 0.000 0.190
243 1 3 242 244 255 0 1.341 1.333 1.103 3.783 0.000 -0.063
244 1 3 243 245 256 0 1.333 1.303 1.350 3.985 0.000 0.194
245 1 3 244 246 257 0 1.303 1.313 1.161 3.784 0.000 -0.066
246 1 3 245 241 258 0 1.313 1.328 1.344 3.985 0.000 0.188
247 2 2 254 260 0 0.855 0.269 1.123 0.000 0.366
248 2 2 254 261 0 0.878 0.236 1.114 0.000 0.387
249 2 2 262 256 0 0.232 0.885 1.116 0.000 0.380
250 2 2 256 263 0 0.827 0.291 1.118 0.000 0.385
251 2 2 258 264 0 0.852 0.273 1.124 0.000 0.377
252 2 2 258 259 0 0.862 0.262 1.125 0.000 0.387
254 4 3 247 248 242 0 0.855 0.878 1.325 3.058 0.977 -0.457
255 4 3 243 261 262 0 1.103 1.245 1.247 3.595 0.081 0.390
256 4 3 244 249 250 0 1.350 0.885 0.827 3.061 0.974 -0.433
257 4 3 245 263 264 0 1.161 1.206 1.224 3.591 0.084 0.359
258 4 3 246 251 252 0 1.344 0.852 0.862 3.058 0.977 -0.427
261 3 2 255 248 0 1.245 0.236 1.491 2.000 -0.389
262 3 2 249 255 0 0.232 1.247 1.489 2.000 -0.415
263 3 2 250 257 0 0.291 1.206 1.508 2.000 -0.397
264 3 2 251 257 0 0.273 1.224 1.507 2.000 -0.422
265 1 3 266 270 277 0 1.321 1.328 1.129 3.783 0.000 -0.075
266 1 3 265 267 278 0 1.321 1.341 1.325 3.987 0.000 0.190
267 1 3 266 268 279 0 1.341 1.333 1.103 3.783 0.000 -0.063
268 1 3 267 269 280 0 1.333 1.303 1.350 3.985 0.000 0.194
269 1 3 268 270 281 0 1.303 1.313 1.161 3.784 0.000 -0.066
270 1 3 265 269 282 0 1.328 1.313 1.344 3.985 0.000 0.188
271 2 2 278 284 0 0.855 0.269 1.123 0.000 0.366
272 2 2 278 285 0 0.878 0.236 1.114 0.000 0.387
273 2 2 280 286 0 0.885 0.232 1.116 0.000 0.380
274 2 2 287 280 0 0.291 0.827 1.118 0.000 0.385
275 2 2 282 288 0 0.852 0.273 1.124 0.000 0.377
276 2 2 282 283 0 0.862 0.262 1.125 0.000 0.387
277 4 3 265 283 284 0 1.129 1.231 1.232 3.591 0.083 0.362
278 4 3 266 271 272 0 1.325 0.855 0.878 3.058 0.977 -0.457
279 4 3 267 285 286 0 1.103 1.245 1.247 3.595 0.081 0.390
280 4 3 273 274 268 0 0.885 0.827 1.350 3.061 0.974 -0.433
281 4 3 269 287 288 0 1.161 1.206 1.224 3.591 0.084 0.359
282 4 3 270 275 276 0 1.344 0.852 0.862 3.058 0.977 -0.427
283 3 2 276 277 0 0.262 1.231 1.504 2.000 -0.395
284 3 2 271 277 0 0.269 1.232 1.511 2.000 -0.426
285 3 2 279 272 0 1.245 0.236 1.491 2.000 -0.389
286 3 2 273 279 0 0.232 1.247 1.489 2.000 -0.415
287 3 2 281 274 0 1.206 0.291 1.508 2.000 -0.397
288 3 2 275 281 0 0.273 1.224 1.507 2.000 -0.422
289 1 3 290 294 301 0 1.321 1.328 1.129 3.783 0.000 -0.075
290 1 3 289 291 302 0 1.321 1.341 1.325 3.987 0.000 0.190
291 1 3 290 303 292 0 1.341 1.103 1.333 3.783 0.000 -0.063
292 1 3 291 293 304 0 1.333 1.303 1.350 3.985 0.000 0.194
293 1 3 292 294 305 0 1.303 1.313 1.161 3.784 0.000 -0.066
294 1 3 289 293 306 0 1.328 1.313 1.344 3.985 0.000 0.188
295 2 2 302 308 0 0.855 0.269 1.123 0.000 0.366
296 2 2 302 309 0 0.878 0.236 1.114 0.000 0.387
297 2 2 310 304 0 0.232 0.885 1.116 0.000 0.380
298 2 2 311 304 0 0.291 0.827 1.118 0.000 0.385
299 2 2 312 306 0 0.273 0.852 1.124 0.000 0.377
300 2 2 306 307 0 0.862 0.262 1.125 0.000 0.387
301 4 3 289 308 307 0 1.129 1.232 1.231 3.591 0.083 0.362
302 4 3 290 295 296 0 1.325 0.855 0.878 3.058 0.977 -0.457
303 4 3 291 309 310 0 1.103 1.245 1.247 3.595 0.081 0.390
304 4 3 292 297 298 0 1.350 0.885 0.827 3.061 0.974 -0.433
305 4 3 293 311 312 0 1.161 1.206 1.224 3.591 0.084 0.359
306 4 3 294 299 300 0 1.344 0.852 0.862 3.058 0.977 -0.427
307 3 2 300 301 0 0.262 1.231 1.504 2.000 -0.395
308 3 2 295 301 0 0.269 1.232 1.511 2.000 -0.426
309 3 2 296 303 0 0.236 1.245 1.491 2.000 -0.389
310 3 2 297 303 0 0.232 1.247 1.489 2.000 -0.415
311 3 2 298 305 0 0.291 1.206 1.508 2.000 -0.397
312 3 2 299 305 0 0.273 1.224 1.507 2.000 -0.422
313 1 3 314 318 325 0 1.321 1.328 1.129 3.783 0.000 -0.075
314 1 3 313 315 326 0 1.321 1.341 1.325 3.987 0.000 0.190
315 1 3 314 316 327 0 1.341 1.333 1.103 3.783 0.000 -0.063
316 1 3 315 317 328 0 1.333 1.303 1.350 3.985 0.000 0.194
317 1 3 316 318 329 0 1.303 1.313 1.161 3.784 0.000 -0.066
318 1 3 313 317 330 0 1.328 1.313 1.344 3.985 0.000 0.188
319 2 2 332 326 0 0.269 0.855 1.123 0.000 0.366
320 2 2 326 333 0 0.878 0.236 1.114 0.000 0.387
321 2 2 328 334 0 0.885 0.232 1.116 0.000 0.380
322 2 2 335 328 0 0.291 0.827 1.118 0.000 0.385
323 2 2 330 336 0 0.852 0.273 1.124 0.000 0.377
324 2 2 330 331 0 0.862 0.262 1.125 0.000 0.387
325 4 3 313 331 332 0 1.129 1.231 1.232 3.591 0.083 0.362
326 4 3 314 320 319 0 1.325 0.878 0.855 3.058 0.977 -0.457
327 4 3 315 333 334 0 1.103 1.245 1.247 3.595 0.081 0.390
328 4 3 321 322 316 0 0.885 0.827 1.350 3.061 0.974 -0.433
329 4 3 317 335 336 0 1.161 1.206 1.224 3.591 0.084 0.359
330 4 3 318 323 324 0 1.344 0.852 0.862 3.058 0.977 -0.427
331 3 2 324 325 0 0.262 1.231 1.504 2.000 -0.395
332 3 2 319 325 0 0.269 1.232 1.511 2.000 -0.426
333 3 2 327 320 0 1.245 0.236 1.491 2.000 -0.389
334 3 2 321 327 0 0.232 1.247 1.489 2.000 -0.415
335 3 2 329 322 0 1.206 0.291 1.508 2.000 -0.397
336 3 2 323 329 0 0.273 1.224 1.507 2.000 -0.422
337 1 3 338 342 349 0 1.321 1.328 1.129 3.783 0.000 -0.075
338 1 3 337 339 350 0 1.321 1.341 1.325 3.987 0.000 0.190
339 1 3 338 351 340 0 1.341 1.103 1.333 3.783 0.000 -0.063
340 1 3 339 341 352 0 1.333 1.303 1.350 3.985 0.000 0.194
341 1 3 340 342 353 0 1.303 1.313 1.161 3.784 0.000 -0.066
342 1 3 337 341 354 0 1.328 1.313 1.344 3.985 0.000 0.188
343 2 2 350 356 0 0.855 0.269 1.123 0.000 0.366
344 2 2 350 357 0 0.878 0.236 1.114 0.000 0.387
345 2 2 358 352 0 0.232 0.885 1.116 0.000 0.380
346 2 2 352 359 0 0.827 0.291 1.118 0.000 0.385
347 2 2 360 354 0 0.273 0.852 1.124 0.000 0.377
348 2 2 354 355 0 0.862 0.262 1.125 0.000 0.387
350 4 3 338 343 344 0 1.325 0.855 0.878 3.058 0.977 -0.457
351 4 3 339 357 358 0 1.103 1.245 1.247 3.595 0.081 0.390
352 4 3 340 345 346 0 1.350 0.885 0.827 3.061 0.974 -0.433
353 4 3 341 360 359 0 1.161 1.224 1.206 3.591 0.084 0.359
354 4 3 342 347 348 0 1.344 0.852 0.862 3.058 0.977 -0.427
357 3 2 344 351 0 0.236 1.245 1.491 2.000 -0.389
358 3 2 345 351 0 0.232 1.247 1.489 2.000 -0.415
359 3 2 346 353 0 0.291 1.206 1.508 2.000 -0.397
360 3 2 347 353 0 0.273 1.224 1.507 2.000 -0.422
361 1 3 362 366 373 0 1.321 1.328 1.129 3.783 0.000 -0.075
362 1 3 361 363 374 0 1.321 1.341 1.325 3.987 0.000 0.190
363 1 3 362 364 375 0 1.341 1.333 1.103 3.783 0.000 -0.063
364 1 3 363 365 376 0 1.333 1.303 1.350 3.985 0.000 0.194
365 1 3 364 366 377 0 1.303 1.313 1.161 3.784 0.000 -0.066
366 1 3 361 365 378 0 1.328 1.313 1.344 3.985 0.000 0.188
367 2 2 380 374 0 0.269 0.855 1.123 0.000 0.366
368 2 2 374 381 0 0.878 0.236 1.114 0.000 0.387
369 2 2 376 382 0 0.885 0.232 1.116 0.000 0.380
370 2 2 383 376 0 0.291 0.827 1.118 0.000 0.385
371 2 2 378 384 0 0.852 0.273 1.124 0.000 0.377
372 2 2 378 379 0 0.862 0.262 1.125 0.000 0.387
373 4 3 361 379 380 0 1.129 1.231 1.232 3.591 0.083 0.362
374 4 3 362 368 367 0 1.325 0.878 0.855 3.058 0.977 -0.457
375 4 3 363 381 382 0 1.103 1.245 1.247 3.595 0.081 0.390
376 4 3 369 370 364 0 0.885 0.827 1.350 3.061 0.974 -0.433
377 4 3 365 383 384 0 1.161 1.206 1.224 3.591 0.084 0.359
378 4 3 366 371 372 0 1.344 0.852 0.862 3.058 0.977 -0.427
379 3 2 372 373 0 0.262 1.231 1.504 2.000 -0.395
380 3 2 367 373 0 0.269 1.232 1.511 2.000 -0.426
381 3 2 375 368 0 1.245 0.236 1.491 2.000 -0.389
382 3 2 369 375 0 0.232 1.247 1.489 2.000 -0.415
383 3 2 377 370 0 1.206 0.291 1.508 2.000 -0.397
384 3 2 371 377 0 0.273 1.224 1.507 2.000 -0.422
61 4 3 49 68 67 0 1.129 1.232 1.231 3.591 0.083 0.362
67 3 2 60 61 0 0.262 1.231 1.504 2.000 -0.395
68 3 2 55 61 0 0.269 1.232 1.511 2.000 -0.426
157 4 3 145 164 163 0 1.129 1.232 1.231 3.591 0.083 0.362
163 3 2 157 156 0 1.231 0.262 1.504 2.000 -0.395
164 3 2 151 157 0 0.269 1.232 1.511 2.000 -0.426
253 4 3 241 260 259 0 1.129 1.232 1.231 3.591 0.083 0.362
259 3 2 253 252 0 1.231 0.262 1.504 2.000 -0.395
260 3 2 247 253 0 0.269 1.232 1.511 2.000 -0.426
349 4 3 337 356 355 0 1.129 1.232 1.231 3.591 0.083 0.362
355 3 2 348 349 0 0.262 1.231 1.504 2.000 -0.395
356 3 2 343 349 0 0.269 1.232 1.511 2.000 -0.426
#

801
tools/reax/mol_fra.c
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@ -1,801 +0,0 @@
/*** modified on 12/09/2010 by Aidan Thompson ***/
/*** modified on 10/21/2010 by avv/cfdrc ***/
/*** this code was given to LAMMPS by Sergey Zybin, CalTech ***/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#define Cutoff "Cutoff.dic"
#define Snapshots "bonds.reax"
#define Output1 "fra.out"
#define Output2 "mol.out"
#define Output3 "num.out"
#define Output4 "dipol.out"
#define Output5 "vibtemp.out"
#define Output6 "conc.out"
#define MaxNumBonds 10 //Max Number of bonds per atom
#define MaxMolTypes 80000 //Max Number of molecule types
#define Natomtypes 4 //C,H,O,N
#define Carbon 0
#define Hydrogen 1
#define Nitrogen 3
#define Oxygen 2
// Prototypes for functions
void FileOpenError(FILE *fp,char *name);
void Allocation();
int AtomIndicator(char *symbol);
void SkipLine(FILE *fp);
int Natom,Nmolecule;//total numbers of atoms and molecules
int Nmoltype=0;//number of species
int *Atomdic;//this array stores atom type accessible by atom id-1.
int *MolName;//an array that stores number of atoms of each type for each molecule by using counters of Natomtypes*imoleculetypes+atomtype so if H2 is the second molecule entry the array will have 4=0, 5=2, 6=0, 7=0.
int *MolType;//array with the same info as MolName but accessed by Nmoltype, not molecule id.
int *Mol;//an array that stores the molecule id for each atom
int *NMol;//an array that stores the number of molecules of this species for this frame
double *Netc;//an array that stores charge
double Mass[Natomtypes];
double *rx,*ry,*rz,*Charge;
double *vx,*vy,*vz;
double COdic[Natomtypes][Natomtypes];
double latc_x[3],latc_y[3],latc_z[3];//lattice parameters of the box read from config.out
double Ilatc_x[3],Ilatc_y[3],Ilatc_z[3];//normalized box lengths
double Origin[3];//origin coordinates of the box
FILE *trj,*dpol,*vtemp,*conc;
main() {
void GetAtomlist();
void GetAtomlist_mod();
void GetCOdict();
void AnalyzeTrajectory();
void PostProcess();
GetAtomlist_mod(Snapshots);
GetCOdict(Cutoff);
AnalyzeTrajectory(Snapshots,Output3);
PostProcess(Output1,Output2,Output3);
}
void GetAtomlist_mod(char *name) {
/*This subroutine reads the bonds.petn file to set the number of atoms. It also checks that a full frame exists because it loops over the first frame to populate the Atomdic with the proper type for each atom id.*/
FILE *fp;
char buffer[1000];
int i,j, Nlink, iatom, itemp, id;
double BO,dtemp;//BO is bond order
fp=fopen(name,"r");
FileOpenError(fp,name);
while(fscanf(fp,"%s",buffer)!=EOF) {
if(strcmp(buffer,"particles")==0) {
fscanf(fp,"%d",&Natom);
printf("# of atoms : %d\n",Natom);
Allocation();
}
if(strcmp(buffer,"q")==0) {
for(i=0;i<Natom;i++) {
fscanf(fp,"%d",&iatom);
iatom--;
fscanf(fp,"%d",&itemp);
itemp--;
if (itemp == Carbon){
sprintf(buffer, "C");
}else if(itemp == Hydrogen) {
sprintf(buffer, "H");
}else if(itemp == Oxygen) {
sprintf(buffer, "O");
}else if(itemp == Nitrogen) {
sprintf(buffer, "N");
}
fscanf(fp,"%d",&Nlink);
for(j=0;j<Nlink;j++) {
fscanf(fp,"%d",&itemp);
itemp--;
}
fscanf(fp,"%d",&itemp);
for(j=0;j<Nlink;j++) {
fscanf(fp,"%lf",&BO);
}
fscanf(fp,"%lf",&dtemp);
fscanf(fp,"%lf",&dtemp);
fscanf(fp,"%lf",&dtemp);
id=AtomIndicator(buffer);
Atomdic[iatom]=id;
}
if (i == Natom) goto Ending;
}
}
Ending:;
}
void GetAtomlist(char *name) {
/*This subroutine reads the head of the configuration file to set the lattice parameters and the number of atoms. It also checks that a full frame exists because it loops over the first frame to populate the Atomdic with the proper type for each atom id.*/
FILE *fp;
int i,iatom,count=0,itemp,id,flag;
double dtemp;
double a,b,c,d,e,f,g,h,ii,det;
char buffer[1000];
FILE *temp;
fp=fopen(name,"r");
FileOpenError(fp,name);
while(fscanf(fp,"%s",buffer)!=EOF) {
if(strcmp(buffer,"vectors:")==0) {
fscanf(fp,"%s",buffer);
for(i=0;i<3;i++) fscanf(fp,"%lf",&latc_x[i]);
fscanf(fp,"%s",buffer);
for(i=0;i<3;i++) fscanf(fp,"%lf",&latc_y[i]);
fscanf(fp,"%s",buffer);
for(i=0;i<3;i++) fscanf(fp,"%lf",&latc_z[i]);
}
else if(strcmp(buffer,"origin:")==0) {
fscanf(fp,"%s",buffer);
for(i=0;i<3;i++) fscanf(fp,"%lf",&Origin[i]);
}
else if(strcmp(buffer,"particles")==0) {
fscanf(fp,"%d",&Natom);
printf("# of atoms : %d\n",Natom);
Allocation();
}
else if(strcmp(buffer,"positions")==0) {
for(i=0,flag=0;i<Natom;i++) {
fscanf(fp,"%d",&id);
id--;
fscanf(fp,"%s",buffer);
iatom=AtomIndicator(buffer);
Atomdic[id]=iatom;
count++;
// fscanf(fp,"%d",&itemp);
// fprintf(temp,"\t%d",itemp);
// fscanf(fp,"%lf",&dtemp);
// fprintf(temp,"\t%lf",dtemp);
// fscanf(fp,"%lf",&dtemp);
// fprintf(temp,"\t%lf",dtemp);
// fscanf(fp,"%lf",&dtemp);
// fprintf(temp,"\t%lf",dtemp);
// fscanf(fp,"%lf",&dtemp);
// fprintf(temp,"\t%lf\n",dtemp);
fgets(buffer,1000,fp);
flag=1;
/* fscanf(fp,"%lf",&dtemp); */
/* fscanf(fp,"%lf",&dtemp); */
/* fscanf(fp,"%lf",&dtemp); */
/* fscanf(fp,"%lf",&dtemp); */
}
if(flag==1) break;
}
}
if(Natom!=count) {
printf("Can't read whole # of atoms.\n");
exit(0);
}
a=latc_x[0]; b=latc_y[0]; c=latc_z[0];
d=latc_x[1]; e=latc_y[1]; f=latc_z[1];
g=latc_x[2]; h=latc_y[2]; ii=latc_z[2];
det=a*e*ii-a*f*h-d*b*ii+d*c*h+g*b*f-g*c*e;
if (det != 0) {
Ilatc_x[0]=(e*ii-f*h)/det;
Ilatc_x[1]=-(b*ii-c*h)/det;
Ilatc_x[2]=(b*f-c*e)/det;
Ilatc_y[0]=-(d*ii-f*g)/det;
Ilatc_y[1]=(a*ii-c*g)/det;
Ilatc_y[2]=-(a*f-c*d)/det;
Ilatc_z[0]=(e*g-d*h)/det;
Ilatc_z[1]=-(b*g-a*h)/det;
Ilatc_z[2]=(a*e-b*d)/det;
}
close(fp);
}
void GetCOdict(char *name) {
/* This subroutine populates the cut-off dictionary for each bond and throws an error if any possible combination of atoms do not have a specified bond*/
FILE *fp;
int i,j,iatom,jatom;
double cut;
#define BUFLEN 1000
char buffer[BUFLEN];
fp=fopen(name,"r");
FileOpenError(fp,name);
for(i=0;i<Natomtypes;i++) {
for(j=0;j<Natomtypes;j++) COdic[i][j]=-1;
}
while(fscanf(fp,"%s",buffer)!=EOF) {
if (strcmp(buffer,"#") == 0) {
SkipLine(fp);
continue;
}
iatom=AtomIndicator(buffer);
fscanf(fp,"%s",buffer);
jatom=AtomIndicator(buffer);
fscanf(fp,"%lf",&cut);
COdic[iatom][jatom]=cut;
COdic[jatom][iatom]=cut;
}
for(i=0;i<Natomtypes;i++) {
for(j=0;j<Natomtypes;j++) {
if(COdic[i][j]==-1) {
printf("Can't fine a certain pair for cut off dictionary!\n");
exit(0);
}
}
}
close(fp);
}
void AnalyzeTrajectory(char *name,char *name2) {
/***************************************************************************/
/* This subroutine loops through the data both with the bond lists and the position files.
Step 1: It checks the timestep for the bond list and then reads in the position data ensuring that the timesteps match.
Step 2: It loops over the bonds to identify molecules
Step 3: It loops over the molecules to determine name and species.
Step 4: It calculates and writes dipole.out and vibtemp.out.
Step 5: It writes num.out */
/**************************************************************************/
FILE *fp,*out3;//fp is the file with the bond lists. out3 refers to a scratch file to keep track of how many of each type of molecules exist.
int i,j,k,l,iatom,jatom,Nlink,count,iatomtype,jatomtype;
/* jatom is the neighbor, iatom is the self, Nlink is the number of neighbors, count is a running index to identify order of atoms (e.g. atom 5 is on line 38)*/
int frame;
int itemp,Molid;
/*itemp is a generic variable as needed, Molid is the line of the atom (e.g. atom 5 is on line 38 means Molid[4]=37 because of the zero).*/
double BO,dtemp;//BO is bond order
char buffer[1000];
int Cnct[MaxNumBonds];//connectivity table for a given atom
int Nspec,flag_mol,flag_spec,flag_identity,nd,timestep;
/* Nspec is the number of species during this frame. flag_mol is a binary flag with 1 indicating that this atom belongs to this molecule. flag_spec is a binary flag with 1 indicating that a new species has been found. I have no idea what purpose flag_identity serves, but a 1 indicates that flag_spec is 1.
nd is a return value from CheckExistence.*/
int Name[Natomtypes],MolTemp[Natom];
/*Name is a counter for how many atoms of a given type are in this particular molecule. MolTemp is an array that keeps track of molecule id by atom id. For example, if atom 5 belongs to molecule 3 MolTemp[4]=3*/
int CheckExistence();
void GetAtomdata();
void GetCOMDipole();
fp=fopen(name,"r");
FileOpenError(fp,name);
out3=fopen(name2,"w");
FileOpenError(out3,name2);
frame=0;
while(fscanf(fp,"%s",buffer)!=EOF) {
/* Step 1 */
if(strcmp(buffer,"Timestep")==0) {
fscanf(fp,"%d",&timestep);
// GetAtomdata(timestep);
}
/* Step 2 */
if(strcmp(buffer,"q")==0) {
frame++;
count=0;
/* zeroing out the counters */
for(i=0;i<Natom;i++) {
MolTemp[i]=-1;
NMol[i]=1;
}
/* Step 2A reads the atomid as iatom, the first itemp is a discard of the atom type, Nlink is the number of neighbors, and then the loop over all the bonded neighbors is stored in Cnct, and the last itemp is the ignored 0 to mark the end.*/
for(i=0;i<Natom;i++) {
fscanf(fp,"%d",&iatom);
iatom--;
if(MolTemp[iatom]==-1) {
MolTemp[iatom]=count;
count++;
}
fscanf(fp,"%d",&itemp);
fscanf(fp,"%d",&Nlink);
for(j=0;j<Nlink;j++) {
fscanf(fp,"%d",&itemp);
itemp--;
Cnct[j]=itemp;
}
fscanf(fp,"%d",&itemp);
/* Step 2B reads the bond orders from the bond file and assigns atoms to molecules. The first check is if a bond exists. The second check is if i and j already belong to the same molecule. If they don't and j has no molecule, assign it to i's molecule. If they do, then j was assigned to a different number so loop through the molecule list and set all the atoms on that molecule to the new i molecule. Then read and discard the remainder of the line.*/
for(j=0;j<Nlink;j++) {
fscanf(fp,"%lf",&BO);
jatom=Cnct[j];
Molid=MolTemp[jatom];
iatomtype=Atomdic[iatom];
jatomtype=Atomdic[jatom];
if(BO>COdic[iatomtype][jatomtype]) {
if(Molid!=MolTemp[iatom]) {
if(MolTemp[jatom]==-1) MolTemp[jatom]=MolTemp[iatom];
else {
for(k=0;k<Natom;k++) {
if(MolTemp[k]==Molid) MolTemp[k]=MolTemp[iatom];
}
}
}
}
}
fscanf(fp,"%lf",&dtemp);
fscanf(fp,"%lf",&dtemp);
fscanf(fp,"%lf",&dtemp);
}
/* Step 3 builds the chemical formula for each molecule. For each molecule (the for loop over i with count as the maximum), loop over all the atoms.*/
for(i=0;i<MaxMolTypes;i++) Netc[i]=0.0;
for(i=0,Nspec=0,Nmolecule=0;i<count;i++) {
/* Step 3A: if the atom belongs to this molecule, increment the appropriate type counter (e.g. we have another carbon), flip flag_mol to 1, set the Mol value to this molecule, and add the atomic charge to the running charge total. */
for(j=0;j<Natomtypes;j++) Name[j]=0;
for(j=0,flag_mol=0;j<Natom;j++) {
if(MolTemp[j]==i) {
jatom=Atomdic[j];
Name[jatom]++;
flag_mol=1;
Mol[j]=Nmolecule;
Netc[Nmolecule]+=Charge[j];
}
}
/* Step 3B: If this molecule contains any atoms (flag_mol==1), then determine if it is a new species. MolName is populated as new species are found. In one of the least efficient matching mechanisms ever, we walk through all the known species names. If no match is found, the flag_spec is set to 1. A zero flag_spec means that we have a match, increment the appropriate species counter. Otherwise, if we have a zero number of species or a flipped flag_spec, we have a new species and need to populate its name. Then we increment the number of species as appropriate and always add a new molecule.*/
if(flag_mol==1) {
flag_identity=1;
for(k=0;k<Nspec;k++) {
flag_spec=0;
for(l=0;l<Natomtypes;l++) {
if(MolName[Natomtypes*k+l]!=Name[l]) flag_spec=1;
}
if(flag_spec==0) NMol[k]++;
flag_identity*=flag_spec;
}
if(Nspec==0 || flag_identity==1) {
for(l=0;l<Natomtypes;l++) {
MolName[Natomtypes*Nspec+l]=Name[l];
}
Nspec++;
}
Nmolecule++;
}//ends the if(flag_mol==1) loop
}//ends the for i up to count loop
/* Step 4 does the end of frame cleanup including the writes for COM */
fprintf(out3,"%d\t",timestep);
printf("Timestep = %d\n",timestep);
fprintf(dpol,"%d\n",Nmolecule);
fprintf(dpol,"TSTEP %d\n",timestep);
fprintf(vtemp,"%d\n",Nmolecule);
fprintf(vtemp,"TSTEP %d\n",timestep);
fprintf(conc,"TSTEP %d\n",timestep);
fprintf(conc,"%d\n",Nmolecule);
GetCOMDipole(Nmolecule,timestep,frame);
/* Step 5 prints the list of species and their quantities */
fprintf(out3,"%d\t",Nspec);
for(i=0;i<Nspec;i++) {
nd=CheckExistence(i);
fprintf(out3,"%d ",nd);
fprintf(out3,"%d\t",NMol[i]);
}
fprintf(out3,"\n");
}
}
fflush(out3);
fclose(out3);
fclose(fp);
}
int CheckExistence(int id) {
/* The purpose of this function is to have a list of only the species that occur in this frame. */
int i,j,num,molid,itemp;
int flag,flag_identity=1;
for(i=0;i<Nmoltype;i++) {
flag=0;
for(j=0;j<Natomtypes;j++) {
molid=MolType[Natomtypes*i+j];
if(molid!=MolName[Natomtypes*id+j]) flag=1;
}
if(flag==0) return i;
flag_identity*=flag;
}
for(i=0;i<Natomtypes;i++) {
MolType[Natomtypes*Nmoltype+i]=MolName[Natomtypes*id+i];
}
Nmoltype++;
return Nmoltype-1;
}
void FileOpenError(FILE *fp,char *name) {
if(fp==NULL) {
printf("file open error(%s).\n",name);
exit(0);
}
}
void Allocation() {
/* This subroutine sets up most of the important adjustable arrays based on the number of atoms. It also opens the dipole and vibtemp files for writing.*/
int flag=0;
char name[100];
Atomdic=(int *)malloc(Natom*sizeof(int));
Mol=(int *)malloc(Natom*sizeof(int));
MolName=(int *)malloc(Natom*Natomtypes*sizeof(int));
//20Jun07 JLB: I have made the absurdly huge array much smaller
// MolType=(int *)malloc(Natom*MaxMolTypes*sizeof(int));
MolType=(int *)malloc((Natomtypes+20)*MaxMolTypes*sizeof(int));
NMol=(int *)malloc(Natom*sizeof(int));
rx=(double *)malloc(Natom*sizeof(double));
ry=(double *)malloc(Natom*sizeof(double));
rz=(double *)malloc(Natom*sizeof(double));
vx=(double *)malloc(Natom*sizeof(double));
vy=(double *)malloc(Natom*sizeof(double));
vz=(double *)malloc(Natom*sizeof(double));
Charge=(double *)malloc(Natom*sizeof(double));
Netc=(double *)malloc(MaxMolTypes*sizeof(double));
if(Atomdic==NULL || NMol==NULL || Mol==NULL || MolType==NULL) flag=1;
if(rx==NULL || ry==NULL || rz==NULL || Charge==NULL) flag=1;
if(vx==NULL || vy==NULL || vz==NULL) flag=1;
if(Netc==NULL) flag=1;
if(flag==1) {
printf("malloc error.\n");
exit(0);
}
// trj=fopen(Atomlist,"r");
// FileOpenError(trj,Atomlist);
dpol=fopen(Output4,"w");
FileOpenError(dpol,Output4);
vtemp=fopen(Output5,"w");
FileOpenError(vtemp,Output5);
conc=fopen(Output6,"w");
FileOpenError(conc,Output6);
}
int AtomIndicator(char *symbol) {
/* This subroutine identifies the atom type from the config file and sets the masses. Why set the masses here, I don't know.*/
int value;
Mass[Hydrogen]=1.0079;
Mass[Carbon]=12.0107;
Mass[Oxygen]=15.9994;
Mass[Nitrogen]=14.0067;
if(strcmp(symbol,"H")==0) value=Hydrogen;
else if(strcmp(symbol,"C")==0) value=Carbon;
else if(strcmp(symbol,"O")==0) value=Oxygen;
else if(strcmp(symbol,"N")==0) value=Nitrogen;
else {
printf("Can't recognize the atom type : %s.\n",symbol);
exit(0);
}
return value;
}
void PostProcess(char *name,char *name2,char *name3) {
/* This subroutine does the global lists after all the frames have been read. out is the fra.out with the list of species and number of each per frame. out2 is mol.out with the chemical identities of each species. out3 is num.out which is the scratch file with number of species per frame in a non-plottable format.*/
int i,j;
FILE *out,*out2,*out3;
int step,molnum,id,num,itemp;
int numcount[Nmoltype];
out=fopen(name,"w");
FileOpenError(out,name);
out2=fopen(name2,"w");
FileOpenError(out2,name2);
out3=fopen(name3,"r");
FileOpenError(out3,name3);
fprintf(out,"Timestep\t");
fprintf(out2,"%d\n\n",Nmoltype);
/* To get the chemical identity of a species, this process loops over each atom type and writes the number of atoms of that type in the formula. */
for(i=0;i<Nmoltype;i++) {
fprintf(out2,"%d\t",i);
for(j=0;j<Natomtypes;j++) {
itemp=MolType[Natomtypes*i+j];
if(itemp!=0) {
if(j==Carbon) {
fprintf(out,"C");
fprintf(out2,"C");
}
else if(j==Hydrogen) {
fprintf(out,"H");
fprintf(out2,"H");
}
else if(j==Oxygen) {
fprintf(out,"O");
fprintf(out2,"O");
}
else if(j==Nitrogen) {
fprintf(out,"N");
fprintf(out2,"N");
}
if(itemp!=1) {
fprintf(out,"%d",itemp);
fprintf(out2,"%d",itemp);
}
}
}
fprintf(out,"\t");
fprintf(out2,"\n");
}
fprintf(out,"\n");
/* for each molecule type, read the num.out scratch file and find the number of those molecules. Then write it out in a nice column format suitable for plotting. */
while(fscanf(out3,"%d",&step)!=EOF) {
fscanf(out3,"%d",&num);
for(i=0;i<Nmoltype;i++) numcount[i]=0;
for(i=0;i<num;i++) {
fscanf(out3,"%d",&id);
fscanf(out3,"%d",&molnum);
numcount[id]=molnum;
}
fprintf(out,"%d\t",step);
for(i=0;i<Nmoltype;i++) {
fprintf(out,"%d\t",numcount[i]);
}
fprintf(out,"\n");
}
}
void GetAtomdata(int tstep) {
/* This subroutine reads in the position data for a frame*/
int i,iatom,count=0,itemp,id,flag;
double dtemp;
int step;
char buffer[1000];
while(fscanf(trj,"%s",buffer)!=EOF) {
if(strcmp(buffer,"Timestep")==0) {
fscanf(trj,"%d",&step);
if(step!=tstep) {
printf("The sequences are not matched between bond data file and coordinate file\n");
printf("step in config file : %d\tStep in bond file : %d\n",tstep,step);
exit(0);
}
}
else if(strcmp(buffer,"positions")==0) {
for(i=0,flag=0;i<Natom;i++) {
fscanf(trj,"%d",&id);
id--;
fscanf(trj,"%s",buffer);
iatom=AtomIndicator(buffer);
Atomdic[id]=iatom;
fscanf(trj,"%d",&itemp);
fscanf(trj,"%lf",&dtemp);
Charge[id]=dtemp;
fscanf(trj,"%lf",&dtemp);
rx[id]=dtemp;
fscanf(trj,"%lf",&dtemp);
ry[id]=dtemp;
fscanf(trj,"%lf",&dtemp);
rz[id]=dtemp;
fscanf(trj,"%lf",&dtemp);
vx[id]=dtemp;
fscanf(trj,"%lf",&dtemp);
vy[id]=dtemp;
fscanf(trj,"%lf",&dtemp);
vz[id]=dtemp;
fscanf(trj,"%lf",&dtemp);
flag=1;
}
if(flag==1) break;
}
}
}
void GetCOMDipole(int max,int tstep,int frame) {
/* max is the number of molecules */
int i;
void AnalCOMDipole();
for(i=0;i<max;i++) AnalCOMDipole(i);
}
void AnalCOMDipole(int molid) {
int i,j,ix,iy,iz,count,itemp;
int ntot;
double mass,chg;
int atomid;
double totmass;
double x0,y0,z0,xtemp,ytemp,ztemp,x,y,z,r2,minr2,dx,dy,dz;
double COMx,COMy,COMz;
double vCOMx,vCOMy,vCOMz;
double Dpolx,Dpoly,Dpolz,Dpol;
double VibTempx,VibTempy,VibTempz,VibTemp;
int Name[Natomtypes];
double tempx,tempy,tempz;
totmass=0.0;
vCOMx=vCOMy=vCOMz=0.0;
/* Again in an inefficient way, we loop over all the atoms to find the ones that are members of this molecule (molid). Then calculate the desired quantities, including the fact that the first atom sets our standard for measurement. Then, we write the quantities to the COM files.
JB 26Sep07: to facilitate my write out of the chemical formula, redo the molecule determination here. */
for(j=0;j<Natomtypes;j++) Name[j]=0;
for(i=0,count=0;i<Natom;i++) {
if(Mol[i]==molid) {
atomid=Atomdic[i];
Name[atomid]++;
mass=Mass[atomid];
chg=Charge[i];
totmass+=mass;
vCOMx+=mass*vx[i];
vCOMy+=mass*vy[i];
vCOMz+=mass*vz[i];
if(count==0) {
// printf("i, rx[i], ry[i], rz[i] , mass %d %e %e %e %e\n", i, rx[i], ry[i], rz[i] , mass);
x0=rx[i];
y0=ry[i];
z0=rz[i];
COMx=mass*x0;
COMy=mass*y0;
COMz=mass*z0;
}
if(count!=0) {
minr2=1.0e8;
for(ix=-1;ix<2;ix++) {
for(iy=-1;iy<2;iy++) {
for(iz=-1;iz<2;iz++) {
xtemp=rx[i]+ix*latc_x[0]+iy*latc_y[0]+iz*latc_z[0];
ytemp=ry[i]+ix*latc_x[1]+iy*latc_y[1]+iz*latc_z[1];
ztemp=rz[i]+ix*latc_x[2]+iy*latc_y[2]+iz*latc_z[2];
dx=xtemp-x0;
dy=ytemp-y0;
dz=ztemp-z0;
r2=dx*dx+dy*dy+dz*dz;
if(r2<minr2) {
minr2=r2;
x=xtemp;
y=ytemp;
z=ztemp;
}
}
}
}
rx[i]=x;
ry[i]=y;
rz[i]=z;
// printf("AAA i, rx[i], ry[i], rz[i] , mass %d %e %e %e %e\n", i, rx[i], ry[i], rz[i] , mass);
COMx+=mass*x;
COMy+=mass*y;
COMz+=mass*z;
}
count++;
}
}
// printf ("AAA totmass %e\n",totmass);
COMx/=totmass;
COMy/=totmass;
COMz/=totmass;
vCOMx/=totmass;
vCOMy/=totmass;
vCOMz/=totmass;
VibTempx=VibTempy=VibTempz=0.0;
for(i=0,ntot=0,Dpolx=0.0,Dpoly=0.0,Dpolz=0.0;i<Natom;i++) {
if(Mol[i]==molid) {
atomid=Atomdic[i];
mass=Mass[atomid];
chg=Charge[i];
totmass+=mass;
x=rx[i]-COMx;
y=ry[i]-COMy;
z=rz[i]-COMz;
Dpolx+=chg*x;
Dpoly+=chg*y;
Dpolz+=chg*z;
VibTempx+=mass*(vx[i]-vCOMx)*(vx[i]-vCOMx);
VibTempy+=mass*(vy[i]-vCOMy)*(vy[i]-vCOMy);
VibTempz+=mass*(vz[i]-vCOMz)*(vz[i]-vCOMz);
ntot++;
}
}
VibTempx/=(double)ntot;
VibTempy/=(double)ntot;
VibTempz/=(double)ntot;
VibTemp=(VibTempx+VibTempy+VibTempz)/3.0;
VibTemp*=1.2027E+06;
COMx-=Origin[0]; COMy-=Origin[1]; COMz-=Origin[2];
// printf("VVVV %e %e %e\n",Ilatc_x[0],Ilatc_x[1],Ilatc_x[2]);
tempx=Ilatc_x[0]*COMx;
tempx+=Ilatc_x[1]*COMy;
tempx+=Ilatc_x[2]*COMz;
tempy=Ilatc_y[0]*COMx;
tempy+=Ilatc_y[1]*COMy;
tempy+=Ilatc_y[2]*COMz;
tempz=Ilatc_z[0]*COMx;
tempz+=Ilatc_z[1]*COMy;
tempz+=Ilatc_z[2]*COMz;
tempx-=floor(tempx);
tempy-=floor(tempy);
tempz-=floor(tempz);
COMx=latc_x[0]*tempx+latc_y[0]*tempy+latc_z[0]*tempz;
COMy=latc_x[1]*tempx+latc_y[1]*tempy+latc_z[1]*tempz;
COMz=latc_x[2]*tempx+latc_y[2]*tempy+latc_z[2]*tempz;
// printf ("LATICE %e %e %e %e %e %e \n",latc_x[0], tempx, latc_y[0], tempy,latc_z[0],tempz );
COMx+=Origin[0]; COMy+=Origin[1]; COMz+=Origin[2];
Dpolx/=0.2082267;
Dpoly/=0.2082267;
Dpolz/=0.2082267;
Dpol=Dpolx*Dpolx+Dpoly*Dpoly+Dpolz*Dpolz;
Dpol=sqrt(Dpol);
// printf("BBB %e %e %e\n",COMx,COMy,COMz);
fprintf(dpol,"He %e %e %e ",COMx,COMy,COMz);
fprintf(dpol,"%e %e %e %e\n",Dpol,Dpolx,Dpoly,Dpolz);
fprintf(vtemp,"He %e %e %e",COMx,COMy,COMz);
fprintf(vtemp,"%e %e %e %e\n",VibTemp,vCOMx,vCOMy,vCOMz);
/* JB 26Sep07: I am adding the routines that will write the chemical formula and the COM to a separate file for use with the composition profile. Step 1: determine the chemical formula for this molecule.*/
for(j=0;j<Natomtypes;j++) {
itemp=Name[j];
if(itemp!=0) {
if(j==Carbon) {
fprintf(conc,"C");
}
else if(j==Hydrogen) {
fprintf(conc,"H");
}
else if(j==Oxygen) {
fprintf(conc,"O");
}
else if(j==Nitrogen) {
fprintf(conc,"N");
}
if(itemp!=1) {
fprintf(conc,"%d",itemp);
}
}
}
fprintf(conc,"\t");
fprintf(conc,"%e %e %e\n",COMx,COMy,COMz);
}
void SkipLine(FILE *fp) {
int c;
while ((c = getc(fp)) != EOF)
if (c == '\n') break;
}