Polymer simulation with reax potential

_Vandadi_Mobin · May 28, 2019, 9:09pm

Dear Lammps Users,

I am trying to simulate cellulose crystal using reax potential. But when I try to simulate the system using the following file, atoms all move freely and create a sphere-like shape around each other. Could you please tell me what is the problem in my input file that they don’t stay in their location?

Thank you so much for your help.

Input Script

dimension 3

units real

boundary f f f

atom_style charge

neighbor 0.3 bin

neigh_modify delay 1 every 1 check yes

#create geometry

read_data 224cellulose.data

pair_style reax/c lmp_control

pair_coeff * * ffield.reax.mattsson C C C C C C H H H H H H H H H H H H O O O O O O

fix qeqFix all qeq/reax 1 0.0 10.0 1e-6 reax/c

min_style cg

minimize 1.0e-4 1.0e-6 100 1000

fix 1 all nve

fix 2 all temp/csvr 0.0 300.0 100.0 54324

timestep 0.1

thermo 5000

thermo_style custom step temp pe ke etotal

dump 1 all custom 500 file.*.cfg xs ys zs mass type

run 50000

Andrew_Jewett · May 28, 2019, 10:55pm

I am trying to simulate cellulose crystal using reax potential. But when I try to simulate the system using the following file, atoms all move freely and create a sphere-like shape around each other. Could you please tell me what is the problem in my input file that they don't stay in their location?

Difficult to answer this question. If you can supply a small, simple
data file (hopefully with less than 1000 atoms) which reproduces the
problem, somebody MIGHT attempt to run your simulation. I can't
guarantee that I will have time to try it.

Ultimately, the burden of getting your simulation to work rests on you.
I hope it does not sound like I am dismissing your problem.

Andrew

P.S. It sounds like your system is unstable using the REAX force
field. Perhaps this is not surprising? Although I am not familiar
with REAX, my general impression is that the earliest papers that used
the REAX force field used it to model much simpler crystals. Please
forgive the following ignorant question: Is it possible to expect
realistic behavior using REAXFF to describe ALL of the atoms in a
relatively complicated biological molecular system like cellulose?
Have other people used REAX in this way? If so, do they use it to
describe the entire system, or only part of the system? (I would
guess that a more traditional bonded force-field would be used to
describe the behavior of most of the atoms in a complex organic
molecule.) How do people normally use REAX? Perhaps I am the wrong
person to reply to your question. I hope I did not inadvertently
prevent some more knowledgeable person from replying.

_Vandadi_Mobin · May 29, 2019, 12:01am

Hi Andrew,

Thank you for your response. I added a sample data file (2 by 2 by 4 crystal) to the end of this email.

Yes, there has been many papers that used Reax force field in LAMMPS to simulate cellulose (like Dri et. al. 2015 Evaluation of reactive force fields for cellulose). They simulated the whole system using ffield.reax.mattsson.

I tried to learn from the examples in the LAMMPS files, however, I cannot solve this problem. I hoped I could get some help on why this problem happens.

Thank you for your help.

### LAMMPS data file ###
LAMMPS data file created by TopoTools
855 atoms

24 atom types

-0.500000 0.500000 xlo xhi
-0.500000 0.500000 ylo yhi
-0.500000 0.500000 zlo zhi

Masses

1 12.010700 # C1
2 12.010700 # C2
3 12.010700 # C3
4 12.010700 # C4
5 12.010700 # C5
6 12.010700 # C6
7 1.007940 # H1
8 1.007940 # H2
9 1.007940 # H3
10 1.007940 # H4
11 1.007940 # H5
12 1.007940 # H61
13 1.007940 # H62
14 1.007940 # HO1
15 1.007940 # HO2
16 1.007940 # HO3
17 1.007940 # HO4
18 1.007940 # HO6
19 15.999400 # O1
20 15.999400 # O2
21 15.999400 # O3
22 15.999400 # O4
23 15.999400 # O5
24 15.999400 # O6

Atoms # charge

1 1 0.000000 0.148000 -0.342000 0.449000 # C1
2 7 0.000000 1.093000 -0.153000 0.621000 # H1
3 5 0.000000 0.055000 1.296000 -1.279000 # C5
4 11 0.000000 1.004000 1.484000 -1.131000 # H5
5 23 0.000000 -0.528000 0.807000 -0.055000 # O5
6 2 0.000000 -0.032000 -1.499000 -0.536000 # C2
7 8 0.000000 -0.972000 -1.774000 -0.567000 # H2
8 20 0.000000 0.766000 -2.559000 -0.003000 # O2
9 15 0.000000 0.581000 -2.603000 0.955000 # HO2
10 3 0.000000 0.439000 -1.116000 -1.918000 # C3
11 9 0.000000 1.420000 -1.078000 -1.910000 # H3
12 21 0.000000 0.032000 -2.127000 -2.864000 # O3
13 16 0.000000 0.593000 -1.956000 -3.651000 # HO3
14 4 0.000000 -0.082000 0.244000 -2.336000 # C4
15 10 0.000000 -1.041000 0.143000 -2.517000 # H4
16 22 0.000000 0.535000 0.701000 -3.554000 # O4
17 17 0.000000 0.519000 -0.030000 -4.223000 # HO4
18 6 0.000000 -0.662000 2.599000 -1.588000 # C6
19 12 0.000000 -1.576000 2.411000 -1.846000 # H61
20 13 0.000000 -0.676000 3.155000 -0.794000 # H62
21 24 0.000000 -0.001000 3.284000 -2.637000 # O6
22 18 0.000000 -0.569000 4.012000 -2.958000 # HO6
23 1 0.000000 -0.148000 0.342000 5.639000 # C1
24 7 0.000000 -1.093000 0.153000 5.811000 # H1
25 5 0.000000 -0.055000 -1.296000 3.911000 # C5
26 11 0.000000 -1.004000 -1.484000 4.059000 # H5
27 23 0.000000 0.528000 -0.807000 5.135000 # O5
28 2 0.000000 0.032000 1.499000 4.654000 # C2
29 8 0.000000 0.972000 1.774000 4.623000 # H2
30 20 0.000000 -0.766000 2.559000 5.187000 # O2
31 15 0.000000 -0.581000 2.603000 6.145000 # HO2
32 3 0.000000 -0.439000 1.116000 3.272000 # C3
33 9 0.000000 -1.420000 1.078000 3.280000 # H3
34 21 0.000000 -0.032000 2.127000 2.326000 # O3
35 16 0.000000 -0.593000 1.956000 1.539000 # HO3
36 4 0.000000 0.082000 -0.244000 2.855000 # C4
37 10 0.000000 1.041000 -0.143000 2.673000 # H4
38 22 0.000000 -0.535000 -0.701000 1.636000 # O4
39 6 0.000000 0.662000 -2.599000 3.602000 # C6
40 12 0.000000 1.576000 -2.411000 3.344000 # H61
41 13 0.000000 0.676000 -3.155000 4.396000 # H62
42 24 0.000000 0.001000 -3.284000 2.553000 # O6
43 18 0.000000 0.569000 -4.012000 2.232000 # HO6
44 1 0.000000 0.148000 -0.342000 10.829000 # C1
45 7 0.000000 1.093000 -0.153000 11.001000 # H1
46 5 0.000000 0.055000 1.296000 9.101000 # C5
47 11 0.000000 1.004000 1.484000 9.249000 # H5
48 23 0.000000 -0.528000 0.807000 10.325000 # O5
49 2 0.000000 -0.032000 -1.499000 9.844000 # C2
50 8 0.000000 -0.972000 -1.774000 9.813000 # H2
51 20 0.000000 0.766000 -2.559000 10.377000 # O2
52 15 0.000000 0.581000 -2.603000 11.335000 # HO2
53 3 0.000000 0.439000 -1.116000 8.462000 # C3
54 9 0.000000 1.420000 -1.078000 8.470000 # H3
55 21 0.000000 0.032000 -2.127000 7.516000 # O3
56 16 0.000000 0.593000 -1.956000 6.729000 # HO3
57 4 0.000000 -0.082000 0.244000 8.045000 # C4
58 10 0.000000 -1.041000 0.143000 7.863000 # H4
59 22 0.000000 0.535000 0.701000 6.826000 # O4
60 6 0.000000 -0.662000 2.599000 8.792000 # C6
61 12 0.000000 -1.576000 2.411000 8.534000 # H61
62 13 0.000000 -0.676000 3.155000 9.586000 # H62
63 24 0.000000 -0.001000 3.284000 7.743000 # O6
64 18 0.000000 -0.569000 4.012000 7.422000 # HO6
65 1 0.000000 -0.148000 0.342000 16.018999 # C1
66 7 0.000000 -1.093000 0.153000 16.191000 # H1
67 5 0.000000 -0.055000 -1.296000 14.291000 # C5
68 11 0.000000 -1.004000 -1.484000 14.439000 # H5
69 23 0.000000 0.528000 -0.807000 15.515000 # O5
70 2 0.000000 0.032000 1.499000 15.034000 # C2
71 8 0.000000 0.972000 1.774000 15.003000 # H2
72 20 0.000000 -0.766000 2.559000 15.567000 # O2
73 15 0.000000 -0.581000 2.603000 16.525000 # HO2
74 3 0.000000 -0.439000 1.116000 13.652000 # C3
75 9 0.000000 -1.420000 1.078000 13.660000 # H3
76 21 0.000000 -0.032000 2.127000 12.706000 # O3
77 16 0.000000 -0.593000 1.956000 11.919000 # HO3
78 4 0.000000 0.082000 -0.244000 13.234000 # C4
79 10 0.000000 1.041000 -0.143000 13.053000 # H4
80 22 0.000000 -0.535000 -0.701000 12.016000 # O4
81 6 0.000000 0.662000 -2.599000 13.982000 # C6
82 12 0.000000 1.576000 -2.411000 13.724000 # H61
83 13 0.000000 0.676000 -3.155000 14.776000 # H62
84 24 0.000000 0.001000 -3.284000 12.933000 # O6
85 18 0.000000 0.569000 -4.012000 12.612000 # HO6
86 1 0.000000 0.148000 -0.342000 21.209000 # C1
87 7 0.000000 1.093000 -0.153000 21.381001 # H1
88 5 0.000000 0.055000 1.296000 19.481001 # C5
89 11 0.000000 1.004000 1.484000 19.629000 # H5
90 23 0.000000 -0.528000 0.807000 20.705000 # O5
91 2 0.000000 -0.032000 -1.499000 20.224001 # C2
92 8 0.000000 -0.972000 -1.774000 20.193001 # H2
93 20 0.000000 0.766000 -2.559000 20.757000 # O2
94 15 0.000000 0.581000 -2.603000 21.715000 # HO2
95 3 0.000000 0.439000 -1.116000 18.841999 # C3
96 9 0.000000 1.420000 -1.078000 18.850000 # H3
97 21 0.000000 0.032000 -2.127000 17.896000 # O3
98 16 0.000000 0.593000 -1.956000 17.108999 # HO3
99 4 0.000000 -0.082000 0.244000 18.424000 # C4
100 10 0.000000 -1.041000 0.143000 18.243000 # H4
101 22 0.000000 0.535000 0.701000 17.205999 # O4
102 6 0.000000 -0.662000 2.599000 19.172001 # C6
103 12 0.000000 -1.576000 2.411000 18.914000 # H61
104 13 0.000000 -0.676000 3.155000 19.966000 # H62
105 24 0.000000 -0.001000 3.284000 18.122999 # O6
106 18 0.000000 -0.569000 4.012000 17.802000 # HO6
107 1 0.000000 -0.148000 0.342000 26.399000 # C1
108 7 0.000000 -1.093000 0.153000 26.570999 # H1
109 5 0.000000 -0.055000 -1.296000 24.671000 # C5
110 11 0.000000 -1.004000 -1.484000 24.819000 # H5
111 23 0.000000 0.528000 -0.807000 25.895000 # O5
112 2 0.000000 0.032000 1.499000 25.414000 # C2
113 8 0.000000 0.972000 1.774000 25.382999 # H2
114 20 0.000000 -0.766000 2.559000 25.947001 # O2
115 15 0.000000 -0.581000 2.603000 26.905001 # HO2
116 3 0.000000 -0.439000 1.116000 24.032000 # C3
117 9 0.000000 -1.420000 1.078000 24.040001 # H3
118 21 0.000000 -0.032000 2.127000 23.086000 # O3
119 16 0.000000 -0.593000 1.956000 22.299000 # HO3
120 4 0.000000 0.082000 -0.244000 23.615000 # C4
121 10 0.000000 1.041000 -0.143000 23.433001 # H4
122 22 0.000000 -0.535000 -0.701000 22.396000 # O4
123 6 0.000000 0.662000 -2.599000 24.362000 # C6
124 12 0.000000 1.576000 -2.411000 24.104000 # H61
125 13 0.000000 0.676000 -3.155000 25.156000 # H62
126 24 0.000000 0.001000 -3.284000 23.313000 # O6
127 18 0.000000 0.569000 -4.012000 22.992001 # HO6
128 1 0.000000 0.148000 -0.342000 31.589001 # C1
129 7 0.000000 1.093000 -0.153000 31.761000 # H1
130 5 0.000000 0.055000 1.296000 29.861000 # C5
131 11 0.000000 1.004000 1.484000 30.009001 # H5
132 23 0.000000 -0.528000 0.807000 31.084999 # O5
133 2 0.000000 -0.032000 -1.499000 30.604000 # C2
134 8 0.000000 -0.972000 -1.774000 30.573000 # H2
135 20 0.000000 0.766000 -2.559000 31.136999 # O2
136 15 0.000000 0.581000 -2.603000 32.095001 # HO2
137 3 0.000000 0.439000 -1.116000 29.222000 # C3
138 9 0.000000 1.420000 -1.078000 29.230000 # H3
139 21 0.000000 0.032000 -2.127000 28.275999 # O3
140 16 0.000000 0.593000 -1.956000 27.489000 # HO3
141 4 0.000000 -0.082000 0.244000 28.805000 # C4
142 10 0.000000 -1.041000 0.143000 28.622999 # H4
143 22 0.000000 0.535000 0.701000 27.586000 # O4
144 6 0.000000 -0.662000 2.599000 29.552000 # C6
145 12 0.000000 -1.576000 2.411000 29.294001 # H61
146 13 0.000000 -0.676000 3.155000 30.346001 # H62
147 24 0.000000 -0.001000 3.284000 28.503000 # O6
148 18 0.000000 -0.569000 4.012000 28.181999 # HO6
149 1 0.000000 -0.148000 0.342000 36.778999 # C1
150 7 0.000000 -1.093000 0.153000 36.951000 # H1
151 19 0.000000 0.451000 0.632000 37.999001 # O1
152 14 0.000000 1.294000 0.979000 37.804001 # HO1
153 5 0.000000 -0.055000 -1.296000 35.050999 # C5
154 11 0.000000 -1.004000 -1.484000 35.199001 # H5
155 23 0.000000 0.528000 -0.807000 36.275002 # O5
156 2 0.000000 0.032000 1.499000 35.793999 # C2
157 8 0.000000 0.972000 1.774000 35.763000 # H2
158 20 0.000000 -0.766000 2.559000 36.327000 # O2
159 15 0.000000 -0.581000 2.603000 37.285000 # HO2
160 3 0.000000 -0.439000 1.116000 34.411999 # C3
161 9 0.000000 -1.420000 1.078000 34.419998 # H3
162 21 0.000000 -0.032000 2.127000 33.466000 # O3
163 16 0.000000 -0.593000 1.956000 32.679001 # HO3
164 4 0.000000 0.082000 -0.244000 33.993999 # C4
165 10 0.000000 1.041000 -0.143000 33.813000 # H4
166 22 0.000000 -0.535000 -0.701000 32.776001 # O4
167 6 0.000000 0.662000 -2.599000 34.742001 # C6
168 12 0.000000 1.576000 -2.411000 34.484001 # H61
169 13 0.000000 0.676000 -3.155000 35.535999 # H62
170 24 0.000000 0.001000 -3.284000 33.693001 # O6
171 18 0.000000 0.569000 -4.012000 33.372002 # HO6
172 1 0.000000 3.726000 3.707000 3.159000 # C1
173 7 0.000000 4.691000 3.761000 3.322000 # H1
174 5 0.000000 3.601000 5.357000 1.441000 # C5
175 11 0.000000 4.558000 5.565000 1.422000 # H5
176 23 0.000000 3.212000 4.946000 2.739000 # O5
177 2 0.000000 3.402000 2.590000 2.174000 # C2
178 8 0.000000 2.425000 2.492000 2.130000 # H2
179 20 0.000000 3.956000 1.353000 2.616000 # O2
180 15 0.000000 3.771000 1.298000 3.579000 # HO2
181 3 0.000000 3.905000 2.958000 0.794000 # C3
182 9 0.000000 4.879000 3.058000 0.823000 # H3
183 21 0.000000 3.567000 1.899000 -0.084000 # O3
184 16 0.000000 3.719000 2.227000 -0.998000 # HO3
185 4 0.000000 3.264000 4.286000 0.389000 # C4
186 10 0.000000 2.295000 4.187000 0.300000 # H4
187 22 0.000000 3.838000 4.775000 -0.837000 # O4
188 17 0.000000 3.869000 4.040000 -1.501000 # HO4
189 6 0.000000 2.762000 6.641000 1.168000 # C6
190 12 0.000000 1.873000 6.391000 0.879000 # H61
191 13 0.000000 2.681000 7.153000 1.989000 # H62
192 24 0.000000 3.370000 7.448000 0.176000 # O6
193 18 0.000000 3.081000 8.372000 0.338000 # HO6
194 1 0.000000 3.129000 4.441000 8.349000 # C1
195 7 0.000000 2.165000 4.387000 8.512000 # H1
196 5 0.000000 3.255000 2.792000 6.631000 # C5
197 11 0.000000 2.298000 2.583000 6.612000 # H5
198 23 0.000000 3.644000 3.202000 7.929000 # O5
199 2 0.000000 3.453000 5.559000 7.364000 # C2
200 8 0.000000 4.431000 5.657000 7.320000 # H2
201 20 0.000000 2.900000 6.796000 7.806000 # O2
202 15 0.000000 3.084000 6.850000 8.769000 # HO2
203 3 0.000000 2.950000 5.190000 5.984000 # C3
204 9 0.000000 1.976000 5.090000 6.013000 # H3
205 21 0.000000 3.289000 6.250000 5.106000 # O3
206 16 0.000000 3.136000 5.921000 4.192000 # HO3
207 4 0.000000 3.592000 3.862000 5.579000 # C4
208 10 0.000000 4.561000 3.961000 5.490000 # H4
209 22 0.000000 3.017000 3.373000 4.353000 # O4
210 6 0.000000 4.094000 1.507000 6.358000 # C6
211 12 0.000000 4.983000 1.758000 6.069000 # H61
212 13 0.000000 4.175000 0.996000 7.179000 # H62
213 24 0.000000 3.485000 0.701000 5.366000 # O6
214 18 0.000000 3.774000 -0.224000 5.528000 # HO6
215 1 0.000000 3.726000 3.707000 13.539000 # C1
216 7 0.000000 4.691000 3.761000 13.702000 # H1
217 5 0.000000 3.601000 5.357000 11.821000 # C5
218 11 0.000000 4.558000 5.565000 11.802000 # H5
219 23 0.000000 3.212000 4.946000 13.119000 # O5
220 2 0.000000 3.402000 2.590000 12.554000 # C2
221 8 0.000000 2.425000 2.492000 12.510000 # H2
222 20 0.000000 3.956000 1.353000 12.996000 # O2
223 15 0.000000 3.771000 1.298000 13.959000 # HO2
224 3 0.000000 3.905000 2.958000 11.174000 # C3
225 9 0.000000 4.879000 3.058000 11.203000 # H3
226 21 0.000000 3.567000 1.899000 10.296000 # O3
227 16 0.000000 3.719000 2.227000 9.382000 # HO3
228 4 0.000000 3.264000 4.286000 10.769000 # C4
229 10 0.000000 2.295000 4.187000 10.680000 # H4
230 22 0.000000 3.838000 4.775000 9.543000 # O4
231 6 0.000000 2.762000 6.641000 11.548000 # C6
232 12 0.000000 1.873000 6.391000 11.259000 # H61
233 13 0.000000 2.681000 7.153000 12.369000 # H62
234 24 0.000000 3.370000 7.448000 10.556000 # O6
235 18 0.000000 3.081000 8.372000 10.718000 # HO6
236 1 0.000000 3.129000 4.441000 18.729000 # C1
237 7 0.000000 2.165000 4.387000 18.892000 # H1
238 5 0.000000 3.255000 2.792000 17.011000 # C5
239 11 0.000000 2.298000 2.583000 16.992001 # H5
240 23 0.000000 3.644000 3.202000 18.309000 # O5
241 2 0.000000 3.453000 5.559000 17.743999 # C2
242 8 0.000000 4.431000 5.657000 17.700001 # H2
243 20 0.000000 2.900000 6.796000 18.186001 # O2
244 15 0.000000 3.084000 6.850000 19.149000 # HO2
245 3 0.000000 2.950000 5.190000 16.364000 # C3
246 9 0.000000 1.976000 5.090000 16.393000 # H3
247 21 0.000000 3.289000 6.250000 15.486000 # O3
248 16 0.000000 3.136000 5.921000 14.572000 # HO3
249 4 0.000000 3.592000 3.862000 15.959000 # C4
250 10 0.000000 4.561000 3.961000 15.870000 # H4
251 22 0.000000 3.017000 3.373000 14.733000 # O4
252 6 0.000000 4.094000 1.507000 16.738001 # C6
253 12 0.000000 4.983000 1.758000 16.448999 # H61
254 13 0.000000 4.175000 0.996000 17.559000 # H62
255 24 0.000000 3.485000 0.701000 15.746000 # O6
256 18 0.000000 3.774000 -0.224000 15.908000 # HO6
257 1 0.000000 3.726000 3.707000 23.919001 # C1
258 7 0.000000 4.691000 3.761000 24.082001 # H1
259 5 0.000000 3.601000 5.357000 22.201000 # C5
260 11 0.000000 4.558000 5.565000 22.181999 # H5
261 23 0.000000 3.212000 4.946000 23.499001 # O5
262 2 0.000000 3.402000 2.590000 22.934000 # C2
263 8 0.000000 2.425000 2.492000 22.889999 # H2
264 20 0.000000 3.956000 1.353000 23.375999 # O2
265 15 0.000000 3.771000 1.298000 24.339001 # HO2
266 3 0.000000 3.905000 2.958000 21.554001 # C3
267 9 0.000000 4.879000 3.058000 21.583000 # H3
268 21 0.000000 3.567000 1.899000 20.676001 # O3
269 16 0.000000 3.719000 2.227000 19.761999 # HO3
270 4 0.000000 3.264000 4.286000 21.149000 # C4
271 10 0.000000 2.295000 4.187000 21.059999 # H4
272 22 0.000000 3.838000 4.775000 19.923000 # O4
273 6 0.000000 2.762000 6.641000 21.927999 # C6
274 12 0.000000 1.873000 6.391000 21.639000 # H61
275 13 0.000000 2.681000 7.153000 22.749001 # H62
276 24 0.000000 3.370000 7.448000 20.936001 # O6
277 18 0.000000 3.081000 8.372000 21.098000 # HO6
278 1 0.000000 3.129000 4.441000 29.108999 # C1
279 7 0.000000 2.165000 4.387000 29.271999 # H1
280 5 0.000000 3.255000 2.792000 27.391001 # C5
281 11 0.000000 2.298000 2.583000 27.372000 # H5
282 23 0.000000 3.644000 3.202000 28.688999 # O5
283 2 0.000000 3.453000 5.559000 28.124001 # C2
284 8 0.000000 4.431000 5.657000 28.080000 # H2
285 20 0.000000 2.900000 6.796000 28.566000 # O2
286 15 0.000000 3.084000 6.850000 29.528999 # HO2
287 3 0.000000 2.950000 5.190000 26.743999 # C3
288 9 0.000000 1.976000 5.090000 26.773001 # H3
289 21 0.000000 3.289000 6.250000 25.865999 # O3
290 16 0.000000 3.136000 5.921000 24.952000 # HO3
291 4 0.000000 3.592000 3.862000 26.339001 # C4
292 10 0.000000 4.561000 3.961000 26.250000 # H4
293 22 0.000000 3.017000 3.373000 25.113001 # O4
294 6 0.000000 4.094000 1.507000 27.118000 # C6
295 12 0.000000 4.983000 1.758000 26.829000 # H61
296 13 0.000000 4.175000 0.996000 27.938999 # H62
297 24 0.000000 3.485000 0.701000 26.125999 # O6
298 18 0.000000 3.774000 -0.224000 26.288000 # HO6
299 1 0.000000 3.726000 3.707000 34.299000 # C1
300 7 0.000000 4.691000 3.761000 34.462002 # H1
301 5 0.000000 3.601000 5.357000 32.581001 # C5
302 11 0.000000 4.558000 5.565000 32.562000 # H5
303 23 0.000000 3.212000 4.946000 33.879002 # O5
304 2 0.000000 3.402000 2.590000 33.313999 # C2
305 8 0.000000 2.425000 2.492000 33.270000 # H2
306 20 0.000000 3.956000 1.353000 33.756001 # O2
307 15 0.000000 3.771000 1.298000 34.719002 # HO2
308 3 0.000000 3.905000 2.958000 31.934000 # C3
309 9 0.000000 4.879000 3.058000 31.962999 # H3
310 21 0.000000 3.567000 1.899000 31.056000 # O3
311 16 0.000000 3.719000 2.227000 30.142000 # HO3
312 4 0.000000 3.264000 4.286000 31.528999 # C4
313 10 0.000000 2.295000 4.187000 31.440001 # H4
314 22 0.000000 3.838000 4.775000 30.302999 # O4
315 6 0.000000 2.762000 6.641000 32.307999 # C6
316 12 0.000000 1.873000 6.391000 32.019001 # H61
317 13 0.000000 2.681000 7.153000 33.129002 # H62
318 24 0.000000 3.370000 7.448000 31.316000 # O6
319 18 0.000000 3.081000 8.372000 31.478001 # HO6
320 1 0.000000 3.129000 4.441000 39.488998 # C1
321 7 0.000000 2.165000 4.387000 39.652000 # H1
322 19 0.000000 3.761000 4.656000 40.708000 # O1
323 14 0.000000 4.650000 4.860000 40.513000 # HO1
324 5 0.000000 3.255000 2.792000 37.771000 # C5
325 11 0.000000 2.298000 2.583000 37.751999 # H5
326 23 0.000000 3.644000 3.202000 39.069000 # O5
327 2 0.000000 3.453000 5.559000 38.504002 # C2
328 8 0.000000 4.431000 5.657000 38.459999 # H2
329 20 0.000000 2.900000 6.796000 38.945999 # O2
330 15 0.000000 3.084000 6.850000 39.909000 # HO2
331 3 0.000000 2.950000 5.190000 37.124001 # C3
332 9 0.000000 1.976000 5.090000 37.153000 # H3
333 21 0.000000 3.289000 6.250000 36.245998 # O3
334 16 0.000000 3.136000 5.921000 35.332001 # HO3
335 4 0.000000 3.592000 3.862000 36.719002 # C4
336 10 0.000000 4.561000 3.961000 36.630001 # H4
337 22 0.000000 3.017000 3.373000 35.493000 # O4
338 6 0.000000 4.094000 1.507000 37.498001 # C6
339 12 0.000000 4.983000 1.758000 37.209000 # H61
340 13 0.000000 4.175000 0.996000 38.319000 # H62
341 24 0.000000 3.485000 0.701000 36.506001 # O6
342 18 0.000000 3.774000 -0.224000 36.667999 # HO6
343 1 0.000000 7.932000 -0.342000 0.449000 # C1
344 7 0.000000 8.877000 -0.153000 0.621000 # H1
345 5 0.000000 7.839000 1.296000 -1.279000 # C5
346 11 0.000000 8.788000 1.484000 -1.131000 # H5
347 23 0.000000 7.256000 0.807000 -0.055000 # O5
348 2 0.000000 7.752000 -1.499000 -0.536000 # C2
349 8 0.000000 6.812000 -1.774000 -0.567000 # H2
350 20 0.000000 8.550000 -2.559000 -0.003000 # O2
351 15 0.000000 8.365000 -2.603000 0.955000 # HO2
352 3 0.000000 8.223000 -1.116000 -1.918000 # C3
353 9 0.000000 9.204000 -1.078000 -1.910000 # H3
354 21 0.000000 7.816000 -2.127000 -2.864000 # O3
355 16 0.000000 8.377000 -1.956000 -3.651000 # HO3
356 4 0.000000 7.702000 0.244000 -2.336000 # C4
357 10 0.000000 6.743000 0.143000 -2.517000 # H4
358 22 0.000000 8.319000 0.701000 -3.554000 # O4
359 17 0.000000 8.303000 -0.030000 -4.223000 # HO4
360 6 0.000000 7.122000 2.599000 -1.588000 # C6
361 12 0.000000 6.208000 2.411000 -1.846000 # H61
362 13 0.000000 7.108000 3.155000 -0.794000 # H62
363 24 0.000000 7.783000 3.284000 -2.637000 # O6
364 18 0.000000 7.215000 4.012000 -2.958000 # HO6
365 1 0.000000 7.636000 0.342000 5.639000 # C1
366 7 0.000000 6.691000 0.153000 5.811000 # H1
367 5 0.000000 7.729000 -1.296000 3.911000 # C5
368 11 0.000000 6.780000 -1.484000 4.059000 # H5
369 23 0.000000 8.312000 -0.807000 5.135000 # O5
370 2 0.000000 7.816000 1.499000 4.654000 # C2
371 8 0.000000 8.756000 1.774000 4.623000 # H2
372 20 0.000000 7.018000 2.559000 5.187000 # O2
373 15 0.000000 7.203000 2.603000 6.145000 # HO2
374 3 0.000000 7.345000 1.116000 3.272000 # C3
375 9 0.000000 6.364000 1.078000 3.280000 # H3
376 21 0.000000 7.752000 2.127000 2.326000 # O3
377 16 0.000000 7.191000 1.956000 1.539000 # HO3
378 4 0.000000 7.866000 -0.244000 2.855000 # C4
379 10 0.000000 8.825000 -0.143000 2.673000 # H4
380 22 0.000000 7.249000 -0.701000 1.636000 # O4
381 6 0.000000 8.446000 -2.599000 3.602000 # C6
382 12 0.000000 9.360000 -2.411000 3.344000 # H61
383 13 0.000000 8.460000 -3.155000 4.396000 # H62
384 24 0.000000 7.785000 -3.284000 2.553000 # O6
385 18 0.000000 8.353000 -4.012000 2.232000 # HO6
386 1 0.000000 7.932000 -0.342000 10.829000 # C1
387 7 0.000000 8.877000 -0.153000 11.001000 # H1
388 5 0.000000 7.839000 1.296000 9.101000 # C5
389 11 0.000000 8.788000 1.484000 9.249000 # H5
390 23 0.000000 7.256000 0.807000 10.325000 # O5
391 2 0.000000 7.752000 -1.499000 9.844000 # C2
392 8 0.000000 6.812000 -1.774000 9.813000 # H2
393 20 0.000000 8.550000 -2.559000 10.377000 # O2
394 15 0.000000 8.365000 -2.603000 11.335000 # HO2
395 3 0.000000 8.223000 -1.116000 8.462000 # C3
396 9 0.000000 9.204000 -1.078000 8.470000 # H3
397 21 0.000000 7.816000 -2.127000 7.516000 # O3
398 16 0.000000 8.377000 -1.956000 6.729000 # HO3
399 4 0.000000 7.702000 0.244000 8.045000 # C4
400 10 0.000000 6.743000 0.143000 7.863000 # H4
401 22 0.000000 8.319000 0.701000 6.826000 # O4
402 6 0.000000 7.122000 2.599000 8.792000 # C6
403 12 0.000000 6.208000 2.411000 8.534000 # H61
404 13 0.000000 7.108000 3.155000 9.586000 # H62
405 24 0.000000 7.783000 3.284000 7.743000 # O6
406 18 0.000000 7.215000 4.012000 7.422000 # HO6
407 1 0.000000 7.636000 0.342000 16.018999 # C1
408 7 0.000000 6.691000 0.153000 16.191000 # H1
409 5 0.000000 7.729000 -1.296000 14.291000 # C5
410 11 0.000000 6.780000 -1.484000 14.439000 # H5
411 23 0.000000 8.312000 -0.807000 15.515000 # O5
412 2 0.000000 7.816000 1.499000 15.034000 # C2
413 8 0.000000 8.756000 1.774000 15.003000 # H2
414 20 0.000000 7.018000 2.559000 15.567000 # O2
415 15 0.000000 7.203000 2.603000 16.525000 # HO2
416 3 0.000000 7.345000 1.116000 13.652000 # C3
417 9 0.000000 6.364000 1.078000 13.660000 # H3
418 21 0.000000 7.752000 2.127000 12.706000 # O3
419 16 0.000000 7.191000 1.956000 11.919000 # HO3
420 4 0.000000 7.866000 -0.244000 13.234000 # C4
421 10 0.000000 8.825000 -0.143000 13.053000 # H4
422 22 0.000000 7.249000 -0.701000 12.016000 # O4
423 6 0.000000 8.446000 -2.599000 13.982000 # C6
424 12 0.000000 9.360000 -2.411000 13.724000 # H61
425 13 0.000000 8.460000 -3.155000 14.776000 # H62
426 24 0.000000 7.785000 -3.284000 12.933000 # O6
427 18 0.000000 8.353000 -4.012000 12.612000 # HO6
428 1 0.000000 7.932000 -0.342000 21.209000 # C1
429 7 0.000000 8.877000 -0.153000 21.381001 # H1
430 5 0.000000 7.839000 1.296000 19.481001 # C5
431 11 0.000000 8.788000 1.484000 19.629000 # H5
432 23 0.000000 7.256000 0.807000 20.705000 # O5
433 2 0.000000 7.752000 -1.499000 20.224001 # C2
434 8 0.000000 6.812000 -1.774000 20.193001 # H2
435 20 0.000000 8.550000 -2.559000 20.757000 # O2
436 15 0.000000 8.365000 -2.603000 21.715000 # HO2
437 3 0.000000 8.223000 -1.116000 18.841999 # C3
438 9 0.000000 9.204000 -1.078000 18.850000 # H3
439 21 0.000000 7.816000 -2.127000 17.896000 # O3
440 16 0.000000 8.377000 -1.956000 17.108999 # HO3
441 4 0.000000 7.702000 0.244000 18.424000 # C4
442 10 0.000000 6.743000 0.143000 18.243000 # H4
443 22 0.000000 8.319000 0.701000 17.205999 # O4
444 6 0.000000 7.122000 2.599000 19.172001 # C6
445 12 0.000000 6.208000 2.411000 18.914000 # H61
446 13 0.000000 7.108000 3.155000 19.966000 # H62
447 24 0.000000 7.783000 3.284000 18.122999 # O6
448 18 0.000000 7.215000 4.012000 17.802000 # HO6
449 1 0.000000 7.636000 0.342000 26.399000 # C1
450 7 0.000000 6.691000 0.153000 26.570999 # H1
451 5 0.000000 7.729000 -1.296000 24.671000 # C5
452 11 0.000000 6.780000 -1.484000 24.819000 # H5
453 23 0.000000 8.312000 -0.807000 25.895000 # O5
454 2 0.000000 7.816000 1.499000 25.414000 # C2
455 8 0.000000 8.756000 1.774000 25.382999 # H2
456 20 0.000000 7.018000 2.559000 25.947001 # O2
457 15 0.000000 7.203000 2.603000 26.905001 # HO2
458 3 0.000000 7.345000 1.116000 24.032000 # C3
459 9 0.000000 6.364000 1.078000 24.040001 # H3
460 21 0.000000 7.752000 2.127000 23.086000 # O3
461 16 0.000000 7.191000 1.956000 22.299000 # HO3
462 4 0.000000 7.866000 -0.244000 23.615000 # C4
463 10 0.000000 8.825000 -0.143000 23.433001 # H4
464 22 0.000000 7.249000 -0.701000 22.396000 # O4
465 6 0.000000 8.446000 -2.599000 24.362000 # C6
466 12 0.000000 9.360000 -2.411000 24.104000 # H61
467 13 0.000000 8.460000 -3.155000 25.156000 # H62
468 24 0.000000 7.785000 -3.284000 23.313000 # O6
469 18 0.000000 8.353000 -4.012000 22.992001 # HO6
470 1 0.000000 7.932000 -0.342000 31.589001 # C1
471 7 0.000000 8.877000 -0.153000 31.761000 # H1
472 5 0.000000 7.839000 1.296000 29.861000 # C5
473 11 0.000000 8.788000 1.484000 30.009001 # H5
474 23 0.000000 7.256000 0.807000 31.084999 # O5
475 2 0.000000 7.752000 -1.499000 30.604000 # C2
476 8 0.000000 6.812000 -1.774000 30.573000 # H2
477 20 0.000000 8.550000 -2.559000 31.136999 # O2
478 15 0.000000 8.365000 -2.603000 32.095001 # HO2
479 3 0.000000 8.223000 -1.116000 29.222000 # C3
480 9 0.000000 9.204000 -1.078000 29.230000 # H3
481 21 0.000000 7.816000 -2.127000 28.275999 # O3
482 16 0.000000 8.377000 -1.956000 27.489000 # HO3
483 4 0.000000 7.702000 0.244000 28.805000 # C4
484 10 0.000000 6.743000 0.143000 28.622999 # H4
485 22 0.000000 8.319000 0.701000 27.586000 # O4
486 6 0.000000 7.122000 2.599000 29.552000 # C6
487 12 0.000000 6.208000 2.411000 29.294001 # H61
488 13 0.000000 7.108000 3.155000 30.346001 # H62
489 24 0.000000 7.783000 3.284000 28.503000 # O6
490 18 0.000000 7.215000 4.012000 28.181999 # HO6
491 1 0.000000 7.636000 0.342000 36.778999 # C1
492 7 0.000000 6.691000 0.153000 36.951000 # H1
493 19 0.000000 8.235000 0.632000 37.999001 # O1
494 14 0.000000 9.078000 0.979000 37.804001 # HO1
495 5 0.000000 7.729000 -1.296000 35.050999 # C5
496 11 0.000000 6.780000 -1.484000 35.199001 # H5
497 23 0.000000 8.312000 -0.807000 36.275002 # O5
498 2 0.000000 7.816000 1.499000 35.793999 # C2
499 8 0.000000 8.756000 1.774000 35.763000 # H2
500 20 0.000000 7.018000 2.559000 36.327000 # O2
501 15 0.000000 7.203000 2.603000 37.285000 # HO2
502 3 0.000000 7.345000 1.116000 34.411999 # C3
503 9 0.000000 6.364000 1.078000 34.419998 # H3
504 21 0.000000 7.752000 2.127000 33.466000 # O3
505 16 0.000000 7.191000 1.956000 32.679001 # HO3
506 4 0.000000 7.866000 -0.244000 33.993999 # C4
507 10 0.000000 8.825000 -0.143000 33.813000 # H4
508 22 0.000000 7.249000 -0.701000 32.776001 # O4
509 6 0.000000 8.446000 -2.599000 34.742001 # C6
510 12 0.000000 9.360000 -2.411000 34.484001 # H61
511 13 0.000000 8.460000 -3.155000 35.535999 # H62
512 24 0.000000 7.785000 -3.284000 33.693001 # O6
513 18 0.000000 8.353000 -4.012000 33.372002 # HO6
514 1 0.000000 -0.780000 7.806000 0.449000 # C1
515 7 0.000000 0.165000 7.995000 0.621000 # H1
516 5 0.000000 -0.874000 9.444000 -1.279000 # C5
517 11 0.000000 0.076000 9.632000 -1.131000 # H5
518 23 0.000000 -1.456000 8.955000 -0.055000 # O5
519 2 0.000000 -0.960000 6.649000 -0.536000 # C2
520 8 0.000000 -1.900000 6.374000 -0.567000 # H2
521 20 0.000000 -0.162000 5.590000 -0.003000 # O2
522 15 0.000000 -0.347000 5.546000 0.955000 # HO2
523 3 0.000000 -0.490000 7.032000 -1.918000 # C3
524 9 0.000000 0.492000 7.070000 -1.910000 # H3
525 21 0.000000 -0.896000 6.022000 -2.864000 # O3
526 16 0.000000 -0.336000 6.193000 -3.651000 # HO3
527 4 0.000000 -1.011000 8.393000 -2.336000 # C4
528 10 0.000000 -1.969000 8.292000 -2.517000 # H4
529 22 0.000000 -0.393000 8.849000 -3.554000 # O4
530 17 0.000000 -0.409000 8.118000 -4.223000 # HO4
531 6 0.000000 -1.590000 10.748000 -1.588000 # C6
532 12 0.000000 -2.505000 10.559000 -1.846000 # H61
533 13 0.000000 -1.605000 11.303000 -0.794000 # H62
534 24 0.000000 -0.929000 11.432000 -2.637000 # O6
535 18 0.000000 -1.498000 12.160000 -2.958000 # HO6
536 1 0.000000 -1.076000 8.491000 5.639000 # C1
537 7 0.000000 -2.022000 8.301000 5.811000 # H1
538 5 0.000000 -0.983000 6.853000 3.911000 # C5
539 11 0.000000 -1.932000 6.664000 4.059000 # H5
540 23 0.000000 -0.401000 7.342000 5.135000 # O5
541 2 0.000000 -0.897000 9.648000 4.654000 # C2
542 8 0.000000 0.043000 9.922000 4.623000 # H2
543 20 0.000000 -1.695000 10.707000 5.187000 # O2
544 15 0.000000 -1.510000 10.751000 6.145000 # HO2
545 3 0.000000 -1.367000 9.265000 3.272000 # C3
546 9 0.000000 -2.349000 9.226000 3.280000 # H3
547 21 0.000000 -0.961000 10.275000 2.326000 # O3
548 16 0.000000 -1.521000 10.104000 1.539000 # HO3
549 4 0.000000 -0.846000 7.904000 2.855000 # C4
550 10 0.000000 0.112000 8.005000 2.673000 # H4
551 22 0.000000 -1.463000 7.448000 1.636000 # O4
552 6 0.000000 -0.266000 5.549000 3.602000 # C6
553 12 0.000000 0.648000 5.737000 3.344000 # H61
554 13 0.000000 -0.252000 4.993000 4.396000 # H62
555 24 0.000000 -0.928000 4.865000 2.553000 # O6
556 18 0.000000 -0.359000 4.136000 2.232000 # HO6
557 1 0.000000 -0.780000 7.806000 10.829000 # C1
558 7 0.000000 0.165000 7.995000 11.001000 # H1
559 5 0.000000 -0.874000 9.444000 9.101000 # C5
560 11 0.000000 0.076000 9.632000 9.249000 # H5
561 23 0.000000 -1.456000 8.955000 10.325000 # O5
562 2 0.000000 -0.960000 6.649000 9.844000 # C2
563 8 0.000000 -1.900000 6.374000 9.813000 # H2
564 20 0.000000 -0.162000 5.590000 10.377000 # O2
565 15 0.000000 -0.347000 5.546000 11.335000 # HO2
566 3 0.000000 -0.490000 7.032000 8.462000 # C3
567 9 0.000000 0.492000 7.070000 8.470000 # H3
568 21 0.000000 -0.896000 6.022000 7.516000 # O3
569 16 0.000000 -0.336000 6.193000 6.729000 # HO3
570 4 0.000000 -1.011000 8.393000 8.045000 # C4
571 10 0.000000 -1.969000 8.292000 7.863000 # H4
572 22 0.000000 -0.393000 8.849000 6.826000 # O4
573 6 0.000000 -1.590000 10.748000 8.792000 # C6
574 12 0.000000 -2.505000 10.559000 8.534000 # H61
575 13 0.000000 -1.605000 11.303000 9.586000 # H62
576 24 0.000000 -0.929000 11.432000 7.743000 # O6
577 18 0.000000 -1.498000 12.160000 7.422000 # HO6
578 1 0.000000 -1.076000 8.491000 16.018999 # C1
579 7 0.000000 -2.022000 8.301000 16.191000 # H1
580 5 0.000000 -0.983000 6.853000 14.291000 # C5
581 11 0.000000 -1.932000 6.664000 14.439000 # H5
582 23 0.000000 -0.401000 7.342000 15.515000 # O5
583 2 0.000000 -0.897000 9.648000 15.034000 # C2
584 8 0.000000 0.043000 9.922000 15.003000 # H2
585 20 0.000000 -1.695000 10.707000 15.567000 # O2
586 15 0.000000 -1.510000 10.751000 16.525000 # HO2
587 3 0.000000 -1.367000 9.265000 13.652000 # C3
588 9 0.000000 -2.349000 9.226000 13.660000 # H3
589 21 0.000000 -0.961000 10.275000 12.706000 # O3
590 16 0.000000 -1.521000 10.104000 11.919000 # HO3
591 4 0.000000 -0.846000 7.904000 13.234000 # C4
592 10 0.000000 0.112000 8.005000 13.053000 # H4
593 22 0.000000 -1.463000 7.448000 12.016000 # O4
594 6 0.000000 -0.266000 5.549000 13.982000 # C6
595 12 0.000000 0.648000 5.737000 13.724000 # H61
596 13 0.000000 -0.252000 4.993000 14.776000 # H62
597 24 0.000000 -0.928000 4.865000 12.933000 # O6
598 18 0.000000 -0.359000 4.136000 12.612000 # HO6
599 1 0.000000 -0.780000 7.806000 21.209000 # C1
600 7 0.000000 0.165000 7.995000 21.381001 # H1
601 5 0.000000 -0.874000 9.444000 19.481001 # C5
602 11 0.000000 0.076000 9.632000 19.629000 # H5
603 23 0.000000 -1.456000 8.955000 20.705000 # O5
604 2 0.000000 -0.960000 6.649000 20.224001 # C2
605 8 0.000000 -1.900000 6.374000 20.193001 # H2
606 20 0.000000 -0.162000 5.590000 20.757000 # O2
607 15 0.000000 -0.347000 5.546000 21.715000 # HO2
608 3 0.000000 -0.490000 7.032000 18.841999 # C3
609 9 0.000000 0.492000 7.070000 18.850000 # H3
610 21 0.000000 -0.896000 6.022000 17.896000 # O3
611 16 0.000000 -0.336000 6.193000 17.108999 # HO3
612 4 0.000000 -1.011000 8.393000 18.424000 # C4
613 10 0.000000 -1.969000 8.292000 18.243000 # H4
614 22 0.000000 -0.393000 8.849000 17.205999 # O4
615 6 0.000000 -1.590000 10.748000 19.172001 # C6
616 12 0.000000 -2.505000 10.559000 18.914000 # H61
617 13 0.000000 -1.605000 11.303000 19.966000 # H62
618 24 0.000000 -0.929000 11.432000 18.122999 # O6
619 18 0.000000 -1.498000 12.160000 17.802000 # HO6
620 1 0.000000 -1.076000 8.491000 26.399000 # C1
621 7 0.000000 -2.022000 8.301000 26.570999 # H1
622 5 0.000000 -0.983000 6.853000 24.671000 # C5
623 11 0.000000 -1.932000 6.664000 24.819000 # H5
624 23 0.000000 -0.401000 7.342000 25.895000 # O5
625 2 0.000000 -0.897000 9.648000 25.414000 # C2
626 8 0.000000 0.043000 9.922000 25.382999 # H2
627 20 0.000000 -1.695000 10.707000 25.947001 # O2
628 15 0.000000 -1.510000 10.751000 26.905001 # HO2
629 3 0.000000 -1.367000 9.265000 24.032000 # C3
630 9 0.000000 -2.349000 9.226000 24.040001 # H3
631 21 0.000000 -0.961000 10.275000 23.086000 # O3
632 16 0.000000 -1.521000 10.104000 22.299000 # HO3
633 4 0.000000 -0.846000 7.904000 23.615000 # C4
634 10 0.000000 0.112000 8.005000 23.433001 # H4
635 22 0.000000 -1.463000 7.448000 22.396000 # O4
636 6 0.000000 -0.266000 5.549000 24.362000 # C6
637 12 0.000000 0.648000 5.737000 24.104000 # H61
638 13 0.000000 -0.252000 4.993000 25.156000 # H62
639 24 0.000000 -0.928000 4.865000 23.313000 # O6
640 18 0.000000 -0.359000 4.136000 22.992001 # HO6
641 1 0.000000 -0.780000 7.806000 31.589001 # C1
642 7 0.000000 0.165000 7.995000 31.761000 # H1
643 5 0.000000 -0.874000 9.444000 29.861000 # C5
644 11 0.000000 0.076000 9.632000 30.009001 # H5
645 23 0.000000 -1.456000 8.955000 31.084999 # O5
646 2 0.000000 -0.960000 6.649000 30.604000 # C2
647 8 0.000000 -1.900000 6.374000 30.573000 # H2
648 20 0.000000 -0.162000 5.590000 31.136999 # O2
649 15 0.000000 -0.347000 5.546000 32.095001 # HO2
650 3 0.000000 -0.490000 7.032000 29.222000 # C3
651 9 0.000000 0.492000 7.070000 29.230000 # H3
652 21 0.000000 -0.896000 6.022000 28.275999 # O3
653 16 0.000000 -0.336000 6.193000 27.489000 # HO3
654 4 0.000000 -1.011000 8.393000 28.805000 # C4
655 10 0.000000 -1.969000 8.292000 28.622999 # H4
656 22 0.000000 -0.393000 8.849000 27.586000 # O4
657 6 0.000000 -1.590000 10.748000 29.552000 # C6
658 12 0.000000 -2.505000 10.559000 29.294001 # H61
659 13 0.000000 -1.605000 11.303000 30.346001 # H62
660 24 0.000000 -0.929000 11.432000 28.503000 # O6
661 18 0.000000 -1.498000 12.160000 28.181999 # HO6
662 1 0.000000 -1.076000 8.491000 36.778999 # C1
663 7 0.000000 -2.022000 8.301000 36.951000 # H1
664 19 0.000000 -0.478000 8.782000 37.999001 # O1
665 14 0.000000 0.366000 9.128000 37.805000 # HO1
666 5 0.000000 -0.983000 6.853000 35.050999 # C5
667 11 0.000000 -1.932000 6.664000 35.199001 # H5
668 23 0.000000 -0.401000 7.342000 36.275002 # O5
669 2 0.000000 -0.897000 9.648000 35.793999 # C2
670 8 0.000000 0.043000 9.922000 35.763000 # H2
671 20 0.000000 -1.695000 10.707000 36.327000 # O2
672 15 0.000000 -1.510000 10.751000 37.285000 # HO2
673 3 0.000000 -1.367000 9.265000 34.411999 # C3
674 9 0.000000 -2.349000 9.226000 34.419998 # H3
675 21 0.000000 -0.961000 10.275000 33.466000 # O3
676 16 0.000000 -1.521000 10.104000 32.679001 # HO3
677 4 0.000000 -0.846000 7.904000 33.993999 # C4
678 10 0.000000 0.112000 8.005000 33.813000 # H4
679 22 0.000000 -1.463000 7.448000 32.776001 # O4
680 6 0.000000 -0.266000 5.549000 34.742001 # C6
681 12 0.000000 0.648000 5.737000 34.484001 # H61
682 13 0.000000 -0.252000 4.993000 35.535999 # H62
683 24 0.000000 -0.928000 4.865000 33.693001 # O6
684 18 0.000000 -0.359000 4.136000 33.372002 # HO6
685 1 0.000000 7.004000 7.806000 0.449000 # C1
686 7 0.000000 7.949000 7.995000 0.621000 # H1
687 5 0.000000 6.910000 9.444000 -1.279000 # C5
688 11 0.000000 7.860000 9.632000 -1.131000 # H5
689 23 0.000000 6.328000 8.955000 -0.055000 # O5
690 2 0.000000 6.824000 6.649000 -0.536000 # C2
691 8 0.000000 5.884000 6.374000 -0.567000 # H2
692 20 0.000000 7.622000 5.590000 -0.003000 # O2
693 15 0.000000 7.437000 5.546000 0.955000 # HO2
694 3 0.000000 7.294000 7.032000 -1.918000 # C3
695 9 0.000000 8.276000 7.070000 -1.910000 # H3
696 21 0.000000 6.888000 6.022000 -2.864000 # O3
697 16 0.000000 7.448000 6.193000 -3.651000 # HO3
698 4 0.000000 6.773000 8.393000 -2.336000 # C4
699 10 0.000000 5.815000 8.292000 -2.517000 # H4
700 22 0.000000 7.391000 8.849000 -3.554000 # O4
701 17 0.000000 7.375000 8.118000 -4.223000 # HO4
702 6 0.000000 6.194000 10.748000 -1.588000 # C6
703 12 0.000000 5.279000 10.559000 -1.846000 # H61
704 13 0.000000 6.179000 11.303000 -0.794000 # H62
705 24 0.000000 6.855000 11.432000 -2.637000 # O6
706 18 0.000000 6.286000 12.160000 -2.958000 # HO6
707 1 0.000000 6.708000 8.491000 5.639000 # C1
708 7 0.000000 5.762000 8.301000 5.811000 # H1
709 5 0.000000 6.801000 6.853000 3.911000 # C5
710 11 0.000000 5.852000 6.664000 4.059000 # H5
711 23 0.000000 7.383000 7.342000 5.135000 # O5
712 2 0.000000 6.887000 9.648000 4.654000 # C2
713 8 0.000000 7.827000 9.922000 4.623000 # H2
714 20 0.000000 6.089000 10.707000 5.187000 # O2
715 15 0.000000 6.274000 10.751000 6.145000 # HO2
716 3 0.000000 6.417000 9.265000 3.272000 # C3
717 9 0.000000 5.435000 9.226000 3.280000 # H3
718 21 0.000000 6.823000 10.275000 2.326000 # O3
719 16 0.000000 6.263000 10.104000 1.539000 # HO3
720 4 0.000000 6.938000 7.904000 2.855000 # C4
721 10 0.000000 7.896000 8.005000 2.673000 # H4
722 22 0.000000 6.321000 7.448000 1.636000 # O4
723 6 0.000000 7.518000 5.549000 3.602000 # C6
724 12 0.000000 8.432000 5.737000 3.344000 # H61
725 13 0.000000 7.532000 4.993000 4.396000 # H62
726 24 0.000000 6.856000 4.865000 2.553000 # O6
727 18 0.000000 7.425000 4.136000 2.232000 # HO6
728 1 0.000000 7.004000 7.806000 10.829000 # C1
729 7 0.000000 7.949000 7.995000 11.001000 # H1
730 5 0.000000 6.910000 9.444000 9.101000 # C5
731 11 0.000000 7.860000 9.632000 9.249000 # H5
732 23 0.000000 6.328000 8.955000 10.325000 # O5
733 2 0.000000 6.824000 6.649000 9.844000 # C2
734 8 0.000000 5.884000 6.374000 9.813000 # H2
735 20 0.000000 7.622000 5.590000 10.377000 # O2
736 15 0.000000 7.437000 5.546000 11.335000 # HO2
737 3 0.000000 7.294000 7.032000 8.462000 # C3
738 9 0.000000 8.276000 7.070000 8.470000 # H3
739 21 0.000000 6.888000 6.022000 7.516000 # O3
740 16 0.000000 7.448000 6.193000 6.729000 # HO3
741 4 0.000000 6.773000 8.393000 8.045000 # C4
742 10 0.000000 5.815000 8.292000 7.863000 # H4
743 22 0.000000 7.391000 8.849000 6.826000 # O4
744 6 0.000000 6.194000 10.748000 8.792000 # C6
745 12 0.000000 5.279000 10.559000 8.534000 # H61
746 13 0.000000 6.179000 11.303000 9.586000 # H62
747 24 0.000000 6.855000 11.432000 7.743000 # O6
748 18 0.000000 6.286000 12.160000 7.422000 # HO6
749 1 0.000000 6.708000 8.491000 16.018999 # C1
750 7 0.000000 5.762000 8.301000 16.191000 # H1
751 5 0.000000 6.801000 6.853000 14.291000 # C5
752 11 0.000000 5.852000 6.664000 14.439000 # H5
753 23 0.000000 7.383000 7.342000 15.515000 # O5
754 2 0.000000 6.887000 9.648000 15.034000 # C2
755 8 0.000000 7.827000 9.922000 15.003000 # H2
756 20 0.000000 6.089000 10.707000 15.567000 # O2
757 15 0.000000 6.274000 10.751000 16.525000 # HO2
758 3 0.000000 6.417000 9.265000 13.652000 # C3
759 9 0.000000 5.435000 9.226000 13.660000 # H3
760 21 0.000000 6.823000 10.275000 12.706000 # O3
761 16 0.000000 6.263000 10.104000 11.919000 # HO3
762 4 0.000000 6.938000 7.904000 13.234000 # C4
763 10 0.000000 7.896000 8.005000 13.053000 # H4
764 22 0.000000 6.321000 7.448000 12.016000 # O4
765 6 0.000000 7.518000 5.549000 13.982000 # C6
766 12 0.000000 8.432000 5.737000 13.724000 # H61
767 13 0.000000 7.532000 4.993000 14.776000 # H62
768 24 0.000000 6.856000 4.865000 12.933000 # O6
769 18 0.000000 7.425000 4.136000 12.612000 # HO6
770 1 0.000000 7.004000 7.806000 21.209000 # C1
771 7 0.000000 7.949000 7.995000 21.381001 # H1
772 5 0.000000 6.910000 9.444000 19.481001 # C5
773 11 0.000000 7.860000 9.632000 19.629000 # H5
774 23 0.000000 6.328000 8.955000 20.705000 # O5
775 2 0.000000 6.824000 6.649000 20.224001 # C2
776 8 0.000000 5.884000 6.374000 20.193001 # H2
777 20 0.000000 7.622000 5.590000 20.757000 # O2
778 15 0.000000 7.437000 5.546000 21.715000 # HO2
779 3 0.000000 7.294000 7.032000 18.841999 # C3
780 9 0.000000 8.276000 7.070000 18.850000 # H3
781 21 0.000000 6.888000 6.022000 17.896000 # O3
782 16 0.000000 7.448000 6.193000 17.108999 # HO3
783 4 0.000000 6.773000 8.393000 18.424000 # C4
784 10 0.000000 5.815000 8.292000 18.243000 # H4
785 22 0.000000 7.391000 8.849000 17.205999 # O4
786 6 0.000000 6.194000 10.748000 19.172001 # C6
787 12 0.000000 5.279000 10.559000 18.914000 # H61
788 13 0.000000 6.179000 11.303000 19.966000 # H62
789 24 0.000000 6.855000 11.432000 18.122999 # O6
790 18 0.000000 6.286000 12.160000 17.802000 # HO6
791 1 0.000000 6.708000 8.491000 26.399000 # C1
792 7 0.000000 5.762000 8.301000 26.570999 # H1
793 5 0.000000 6.801000 6.853000 24.671000 # C5
794 11 0.000000 5.852000 6.664000 24.819000 # H5
795 23 0.000000 7.383000 7.342000 25.895000 # O5
796 2 0.000000 6.887000 9.648000 25.414000 # C2
797 8 0.000000 7.827000 9.922000 25.382999 # H2
798 20 0.000000 6.089000 10.707000 25.947001 # O2
799 15 0.000000 6.274000 10.751000 26.905001 # HO2
800 3 0.000000 6.417000 9.265000 24.032000 # C3
801 9 0.000000 5.435000 9.226000 24.040001 # H3
802 21 0.000000 6.823000 10.275000 23.086000 # O3
803 16 0.000000 6.263000 10.104000 22.299000 # HO3
804 4 0.000000 6.938000 7.904000 23.615000 # C4
805 10 0.000000 7.896000 8.005000 23.433001 # H4
806 22 0.000000 6.321000 7.448000 22.396000 # O4
807 6 0.000000 7.518000 5.549000 24.362000 # C6
808 12 0.000000 8.432000 5.737000 24.104000 # H61
809 13 0.000000 7.532000 4.993000 25.156000 # H62
810 24 0.000000 6.856000 4.865000 23.313000 # O6
811 18 0.000000 7.425000 4.136000 22.992001 # HO6
812 1 0.000000 7.004000 7.806000 31.589001 # C1
813 7 0.000000 7.949000 7.995000 31.761000 # H1
814 5 0.000000 6.910000 9.444000 29.861000 # C5
815 11 0.000000 7.860000 9.632000 30.009001 # H5
816 23 0.000000 6.328000 8.955000 31.084999 # O5
817 2 0.000000 6.824000 6.649000 30.604000 # C2
818 8 0.000000 5.884000 6.374000 30.573000 # H2
819 20 0.000000 7.622000 5.590000 31.136999 # O2
820 15 0.000000 7.437000 5.546000 32.095001 # HO2
821 3 0.000000 7.294000 7.032000 29.222000 # C3
822 9 0.000000 8.276000 7.070000 29.230000 # H3
823 21 0.000000 6.888000 6.022000 28.275999 # O3
824 16 0.000000 7.448000 6.193000 27.489000 # HO3
825 4 0.000000 6.773000 8.393000 28.805000 # C4
826 10 0.000000 5.815000 8.292000 28.622999 # H4
827 22 0.000000 7.391000 8.849000 27.586000 # O4
828 6 0.000000 6.194000 10.748000 29.552000 # C6
829 12 0.000000 5.279000 10.559000 29.294001 # H61
830 13 0.000000 6.179000 11.303000 30.346001 # H62
831 24 0.000000 6.855000 11.432000 28.503000 # O6
832 18 0.000000 6.286000 12.160000 28.181999 # HO6
833 1 0.000000 6.708000 8.491000 36.778999 # C1
834 7 0.000000 5.762000 8.301000 36.951000 # H1
835 19 0.000000 7.306000 8.782000 37.999001 # O1
836 14 0.000000 8.150000 9.128000 37.805000 # HO1
837 5 0.000000 6.801000 6.853000 35.050999 # C5
838 11 0.000000 5.852000 6.664000 35.199001 # H5
839 23 0.000000 7.383000 7.342000 36.275002 # O5
840 2 0.000000 6.887000 9.648000 35.793999 # C2
841 8 0.000000 7.827000 9.922000 35.763000 # H2
842 20 0.000000 6.089000 10.707000 36.327000 # O2
843 15 0.000000 6.274000 10.751000 37.285000 # HO2
844 3 0.000000 6.417000 9.265000 34.411999 # C3
845 9 0.000000 5.435000 9.226000 34.419998 # H3
846 21 0.000000 6.823000 10.275000 33.466000 # O3
847 16 0.000000 6.263000 10.104000 32.679001 # HO3
848 4 0.000000 6.938000 7.904000 33.993999 # C4
849 10 0.000000 7.896000 8.005000 33.813000 # H4
850 22 0.000000 6.321000 7.448000 32.776001 # O4
851 6 0.000000 7.518000 5.549000 34.742001 # C6
852 12 0.000000 8.432000 5.737000 34.484001 # H61
853 13 0.000000 7.532000 4.993000 35.535999 # H62
854 24 0.000000 6.856000 4.865000 33.693001 # O6
855 18 0.000000 7.425000 4.136000 33.372002 # HO6
### End of Data File ###

Andrew_Jewett · June 4, 2019, 2:13am

On a whim I finally decided to try your input files.
After fighting with undefined linker errors for a few minutes, I gave
up trying to install the REAX package, so I never actually tried your
input files.

A couple observations:
The size of your boundary box (defined at the top of the DATA file) is
only 1 Angstrom^3. This is non-sensical. It looks like you attempted
to get around this problem by using "boundary f f f" instead of
"boundary p p p", however this will not do what you want either. (I'm
surprised it even ran.)

https://lammps.sandia.gov/doc/boundary.html

If you want to get rid of periodic boundary conditions, try using
"boundary s s s" instead. However, if you use "boundary s s s", and
the system is not carefully minimized, any numeric explosion will
cause LAMMPS to run out of memory (and in my case, crash my linux OS).

If you ever do want to run a periodic simulation, keep in mind that
your middle layer is half the width of the layers above and below it,
so it will not be possible to build a fully 3D uniform density crystal
if you use this as your unit cell. I don't think that contributed to
your current problems.

...Anyway, you might want to fix the boundary conditions before you
continue working with this DATA file.

Don't know if I helped. That's all I have time for.

Good luck

Andrew