Dear all,
I am trying to create to an amorphous alumina (Al2O3).
I have this error:
RROR: Neighbor page size must be >= 10x the one atom setting (src/neighbor.cpp:255)
Could you please tell me how to fix it?
How to determine n1 and n2?
My input:
units metal
atom_style atomic
read_data Al2O3_Orthognonal_360.data
replicate 2 2 2
velocity all create 5000 87287
pair_style eam/alloy
pair_coeff * * AlO.eam.alloy Al O
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes one 1000 page 2000
fix 1 all nvt temp 5000 5000 0.1
fix 2 all deform 1 x final 0 15.70866 y final 0 14.29263 z final 0 18.1387987 units box
thermo 50
thermo_style custom step cpu temp press ke pe etotal vol
thermo_modify lost ignore
dump 1 all atom 1000 dump.lammpstrj
run 500000
unfix 2
unfix 1
fix 1 all nvt temp 5000 3000 0.1
run 500000
unfix 1
fix 1 all nvt temp 3000 3000 0.1
fix 2 all deform 1 x final 0 14.280600 y final 0 12.993300 z final 0 16.489817 units box
run 500000
unfix 1
unfix 2
fix 1 all nvt temp 3000 3000 0.1
run 500000
unfix 1
fix 1 all nvt temp 3000 300 0.1
run 1000000
undump 1
unfix 1
fix 1 all nvt temp 300 300 0.1
dump 1 all atom 1000 dump2.lammpstrj
thermo_style custom step temp density cpu
run 1000000
write_data new_data.txt
The error message tells you. You have 2x but it should be at least 10x.
But then again for your kind of system the defaults should work unless your data file is incorrect.
I tried to use this:
neigh_modify every 1 delay 0 check yes one 1000 page 10000
But I have this error
ERROR on proc 12: Neighbor list overflow, boost neigh_modify one (src/npair_half_bin_atomonly_newton.cpp:111)
my data file is:
LAMMPS data file created from VNL: Compatible with atom_style atomic.
360 atoms
2 atom types
0.000000 14.280600 xlo xhi
0.000000 12.993300 ylo yhi
0.000000 16.489817 zlo zhi
Masses
1 15.999400 # O
2 26.981500 # Al
Atoms # atomic
1 1 3.108982 0.838155 0.111691
2 1 7.869182 0.838155 0.111691
3 1 12.629382 0.838155 0.111691
4 1 1.651218 7.334805 0.111691
5 1 6.411418 7.334805 0.111691
6 1 11.171618 7.334805 0.111691
7 1 0.728882 5.169254 1.262460
8 1 5.489082 5.169254 1.262460
9 1 10.249282 5.169254 1.262460
10 1 4.031318 11.665904 1.262460
11 1 8.791518 11.665904 1.262460
12 1 13.551718 11.665904 1.262460
13 1 0.922336 0.838155 1.374151
14 1 5.682536 0.838155 1.374151
15 1 10.442736 0.838155 1.374151
16 2 2.380100 2.165550 1.374151
17 2 7.140300 2.165550 1.374151
18 2 11.900500 2.165550 1.374151
19 2 2.380100 6.007409 1.374151
20 2 7.140300 6.007409 1.374151
21 2 11.900500 6.007409 1.374151
22 1 3.837864 7.334805 1.374151
23 1 8.598064 7.334805 1.374151
24 1 13.358264 7.334805 1.374151
25 2 2.380100 8.662200 1.374151
26 2 7.140300 8.662200 1.374151
27 2 11.900500 8.662200 1.374151
28 2 2.380100 12.504059 1.374151
29 2 7.140300 12.504059 1.374151
30 2 11.900500 12.504059 1.374151
31 1 4.031318 3.003704 1.485842
32 1 8.791518 3.003704 1.485842
33 1 13.551718 3.003704 1.485842
34 1 0.728882 9.500354 1.485842
35 1 5.489082 9.500354 1.485842
36 1 10.249282 9.500354 1.485842
37 1 3.108982 0.838155 2.636612
38 1 7.869182 0.838155 2.636612
39 1 12.629382 0.838155 2.636612
40 1 1.651218 7.334805 2.636612
41 1 6.411418 7.334805 2.636612
42 1 11.171618 7.334805 2.636612
43 2 -0.000000 1.676309 2.748303
44 2 4.760200 1.676309 2.748303
45 2 9.520400 1.676309 2.748303
46 1 1.457764 3.003704 2.748303
47 1 6.217964 3.003704 2.748303
48 1 10.978164 3.003704 2.748303
49 2 -0.000000 4.331100 2.748303
50 2 4.760200 4.331100 2.748303
51 2 9.520400 4.331100 2.748303
52 2 -0.000000 8.172959 2.748303
53 2 4.760200 8.172959 2.748303
54 2 9.520400 8.172959 2.748303
55 1 3.302436 9.500354 2.748303
56 1 8.062636 9.500354 2.748303
57 1 12.822836 9.500354 2.748303
58 2 -0.000000 10.827750 2.748303
59 2 4.760200 10.827750 2.748303
60 2 9.520400 10.827750 2.748303
61 1 3.108982 5.169254 2.859994
62 1 7.869182 5.169254 2.859994
63 1 12.629382 5.169254 2.859994
64 1 1.651218 11.665904 2.859994
65 1 6.411418 11.665904 2.859994
66 1 11.171618 11.665904 2.859994
67 1 4.031318 3.003704 4.010763
68 1 8.791518 3.003704 4.010763
69 1 13.551718 3.003704 4.010763
70 1 0.728882 9.500354 4.010763
71 1 5.489082 9.500354 4.010763
72 1 10.249282 9.500354 4.010763
73 2 2.380100 0.000000 4.122454
74 2 7.140300 0.000000 4.122454
75 2 11.900500 0.000000 4.122454
76 2 2.380100 3.841859 4.122454
77 2 7.140300 3.841859 4.122454
78 2 11.900500 3.841859 4.122454
79 1 0.922336 5.169254 4.122454
80 1 5.682536 5.169254 4.122454
81 1 10.442736 5.169254 4.122454
82 2 2.380100 6.496650 4.122454
83 2 7.140300 6.496650 4.122454
84 2 11.900500 6.496650 4.122454
85 2 2.380100 10.338509 4.122454
86 2 7.140300 10.338509 4.122454
87 2 11.900500 10.338509 4.122454
88 1 3.837864 11.665904 4.122454
89 1 8.598064 11.665904 4.122454
90 1 13.358264 11.665904 4.122454
91 1 0.728882 0.838155 4.234145
92 1 5.489082 0.838155 4.234145
93 1 10.249282 0.838155 4.234145
94 1 4.031318 7.334805 4.234145
95 1 8.791518 7.334805 4.234145
96 1 13.551718 7.334805 4.234145
97 1 3.108982 5.169254 5.384914
98 1 7.869182 5.169254 5.384914
99 1 12.629382 5.169254 5.384914
100 1 1.651218 11.665904 5.384914
101 1 6.411418 11.665904 5.384914
102 1 11.171618 11.665904 5.384914
103 1 3.302436 0.838155 5.496606
104 1 8.062636 0.838155 5.496606
105 1 12.822836 0.838155 5.496606
106 2 -0.000000 2.165550 5.496606
107 2 4.760200 2.165550 5.496606
108 2 9.520400 2.165550 5.496606
109 2 -0.000000 6.007409 5.496606
110 2 4.760200 6.007409 5.496606
111 2 9.520400 6.007409 5.496606
112 1 1.457764 7.334805 5.496606
113 1 6.217964 7.334805 5.496606
114 1 10.978164 7.334805 5.496606
115 2 -0.000000 8.662200 5.496606
116 2 4.760200 8.662200 5.496606
117 2 9.520400 8.662200 5.496606
118 2 -0.000000 12.504059 5.496606
119 2 4.760200 12.504059 5.496606
120 2 9.520400 12.504059 5.496606
121 1 1.651218 3.003704 5.608297
122 1 6.411418 3.003704 5.608297
123 1 11.171618 3.003704 5.608297
124 1 3.108982 9.500354 5.608297
125 1 7.869182 9.500354 5.608297
126 1 12.629382 9.500354 5.608297
127 1 0.728882 0.838155 6.759066
128 1 5.489082 0.838155 6.759066
129 1 10.249282 0.838155 6.759066
130 1 4.031318 7.334805 6.759066
131 1 8.791518 7.334805 6.759066
132 1 13.551718 7.334805 6.759066
133 2 2.380100 1.676309 6.870757
134 2 7.140300 1.676309 6.870757
135 2 11.900500 1.676309 6.870757
136 1 3.837864 3.003704 6.870757
137 1 8.598064 3.003704 6.870757
138 1 13.358264 3.003704 6.870757
139 2 2.380100 4.331100 6.870757
140 2 7.140300 4.331100 6.870757
141 2 11.900500 4.331100 6.870757
142 2 2.380100 8.172959 6.870757
143 2 7.140300 8.172959 6.870757
144 2 11.900500 8.172959 6.870757
145 1 0.922336 9.500354 6.870757
146 1 5.682536 9.500354 6.870757
147 1 10.442736 9.500354 6.870757
148 2 2.380100 10.827750 6.870757
149 2 7.140300 10.827750 6.870757
150 2 11.900500 10.827750 6.870757
151 1 0.728882 5.169254 6.982448
152 1 5.489082 5.169254 6.982448
153 1 10.249282 5.169254 6.982448
154 1 4.031318 11.665904 6.982448
155 1 8.791518 11.665904 6.982448
156 1 13.551718 11.665904 6.982448
157 1 1.651218 3.003704 8.133217
158 1 6.411418 3.003704 8.133217
159 1 11.171618 3.003704 8.133217
160 1 3.108982 9.500354 8.133217
161 1 7.869182 9.500354 8.133217
162 1 12.629382 9.500354 8.133217
163 2 -0.000000 -0.000000 8.244908
164 2 4.760200 0.000000 8.244908
165 2 9.520400 0.000000 8.244908
166 2 -0.000000 3.841859 8.244908
167 2 4.760200 3.841859 8.244908
168 2 9.520400 3.841859 8.244908
169 1 3.302436 5.169254 8.244908
170 1 8.062636 5.169254 8.244908
171 1 12.822836 5.169254 8.244908
172 2 -0.000000 6.496650 8.244908
173 2 4.760200 6.496650 8.244908
174 2 9.520400 6.496650 8.244908
175 2 -0.000000 10.338509 8.244908
176 2 4.760200 10.338509 8.244908
177 2 9.520400 10.338509 8.244908
178 1 1.457764 11.665904 8.244908
179 1 6.217964 11.665904 8.244908
180 1 10.978164 11.665904 8.244908
181 1 3.108982 0.838155 8.356599
182 1 7.869182 0.838155 8.356599
183 1 12.629382 0.838155 8.356599
184 1 1.651218 7.334805 8.356599
185 1 6.411418 7.334805 8.356599
186 1 11.171618 7.334805 8.356599
187 1 0.728882 5.169254 9.507369
188 1 5.489082 5.169254 9.507369
189 1 10.249282 5.169254 9.507369
190 1 4.031318 11.665904 9.507369
191 1 8.791518 11.665904 9.507369
192 1 13.551718 11.665904 9.507369
193 1 0.922336 0.838155 9.619060
194 1 5.682536 0.838155 9.619060
195 1 10.442736 0.838155 9.619060
196 2 2.380100 2.165550 9.619060
197 2 7.140300 2.165550 9.619060
198 2 11.900500 2.165550 9.619060
199 2 2.380100 6.007409 9.619060
200 2 7.140300 6.007409 9.619060
201 2 11.900500 6.007409 9.619060
202 1 3.837864 7.334805 9.619060
203 1 8.598064 7.334805 9.619060
204 1 13.358264 7.334805 9.619060
205 2 2.380100 8.662200 9.619060
206 2 7.140300 8.662200 9.619060
207 2 11.900500 8.662200 9.619060
208 2 2.380100 12.504059 9.619060
209 2 7.140300 12.504059 9.619060
210 2 11.900500 12.504059 9.619060
211 1 4.031318 3.003704 9.730751
212 1 8.791518 3.003704 9.730751
213 1 13.551718 3.003704 9.730751
214 1 0.728882 9.500354 9.730751
215 1 5.489082 9.500354 9.730751
216 1 10.249282 9.500354 9.730751
217 1 3.108982 0.838155 10.881520
218 1 7.869182 0.838155 10.881520
219 1 12.629382 0.838155 10.881520
220 1 1.651218 7.334805 10.881520
221 1 6.411418 7.334805 10.881520
222 1 11.171618 7.334805 10.881520
223 2 -0.000000 1.676309 10.993211
224 2 4.760200 1.676309 10.993211
225 2 9.520400 1.676309 10.993211
226 1 1.457764 3.003704 10.993211
227 1 6.217964 3.003704 10.993211
228 1 10.978164 3.003704 10.993211
229 2 -0.000000 4.331100 10.993211
230 2 4.760200 4.331100 10.993211
231 2 9.520400 4.331100 10.993211
232 2 -0.000000 8.172959 10.993211
233 2 4.760200 8.172959 10.993211
234 2 9.520400 8.172959 10.993211
235 1 3.302436 9.500354 10.993211
236 1 8.062636 9.500354 10.993211
237 1 12.822836 9.500354 10.993211
238 2 -0.000000 10.827750 10.993211
239 2 4.760200 10.827750 10.993211
240 2 9.520400 10.827750 10.993211
241 1 3.108982 5.169254 11.104902
242 1 7.869182 5.169254 11.104902
243 1 12.629382 5.169254 11.104902
244 1 1.651218 11.665904 11.104902
245 1 6.411418 11.665904 11.104902
246 1 11.171618 11.665904 11.104902
247 1 4.031318 3.003704 12.255671
248 1 8.791518 3.003704 12.255671
249 1 13.551718 3.003704 12.255671
250 1 0.728882 9.500354 12.255671
251 1 5.489082 9.500354 12.255671
252 1 10.249282 9.500354 12.255671
253 2 2.380100 0.000000 12.367362
254 2 7.140300 0.000000 12.367362
255 2 11.900500 0.000000 12.367362
256 2 2.380100 3.841859 12.367362
257 2 7.140300 3.841859 12.367362
258 2 11.900500 3.841859 12.367362
259 1 0.922336 5.169254 12.367362
260 1 5.682536 5.169254 12.367362
261 1 10.442736 5.169254 12.367362
262 2 2.380100 6.496650 12.367362
263 2 7.140300 6.496650 12.367362
264 2 11.900500 6.496650 12.367362
265 2 2.380100 10.338509 12.367362
266 2 7.140300 10.338509 12.367362
267 2 11.900500 10.338509 12.367362
268 1 3.837864 11.665904 12.367362
269 1 8.598064 11.665904 12.367362
270 1 13.358264 11.665904 12.367362
271 1 0.728882 0.838155 12.479053
272 1 5.489082 0.838155 12.479053
273 1 10.249282 0.838155 12.479053
274 1 4.031318 7.334805 12.479053
275 1 8.791518 7.334805 12.479053
276 1 13.551718 7.334805 12.479053
277 1 3.108982 5.169254 13.629823
278 1 7.869182 5.169254 13.629823
279 1 12.629382 5.169254 13.629823
280 1 1.651218 11.665904 13.629823
281 1 6.411418 11.665904 13.629823
282 1 11.171618 11.665904 13.629823
283 1 3.302436 0.838155 13.741514
284 1 8.062636 0.838155 13.741514
285 1 12.822836 0.838155 13.741514
286 2 -0.000000 2.165550 13.741514
287 2 4.760200 2.165550 13.741514
288 2 9.520400 2.165550 13.741514
289 2 -0.000000 6.007409 13.741514
290 2 4.760200 6.007409 13.741514
291 2 9.520400 6.007409 13.741514
292 1 1.457764 7.334805 13.741514
293 1 6.217964 7.334805 13.741514
294 1 10.978164 7.334805 13.741514
295 2 -0.000000 8.662200 13.741514
296 2 4.760200 8.662200 13.741514
297 2 9.520400 8.662200 13.741514
298 2 -0.000000 12.504059 13.741514
299 2 4.760200 12.504059 13.741514
300 2 9.520400 12.504059 13.741514
301 1 1.651218 3.003704 13.853205
302 1 6.411418 3.003704 13.853205
303 1 11.171618 3.003704 13.853205
304 1 3.108982 9.500354 13.853205
305 1 7.869182 9.500354 13.853205
306 1 12.629382 9.500354 13.853205
307 1 0.728882 0.838155 15.003974
308 1 5.489082 0.838155 15.003974
309 1 10.249282 0.838155 15.003974
310 1 4.031318 7.334805 15.003974
311 1 8.791518 7.334805 15.003974
312 1 13.551718 7.334805 15.003974
313 2 2.380100 1.676309 15.115665
314 2 7.140300 1.676309 15.115665
315 2 11.900500 1.676309 15.115665
316 1 3.837864 3.003704 15.115665
317 1 8.598064 3.003704 15.115665
318 1 13.358264 3.003704 15.115665
319 2 2.380100 4.331100 15.115665
320 2 7.140300 4.331100 15.115665
321 2 11.900500 4.331100 15.115665
322 2 2.380100 8.172959 15.115665
323 2 7.140300 8.172959 15.115665
324 2 11.900500 8.172959 15.115665
325 1 0.922336 9.500354 15.115665
326 1 5.682536 9.500354 15.115665
327 1 10.442736 9.500354 15.115665
328 2 2.380100 10.827750 15.115665
329 2 7.140300 10.827750 15.115665
330 2 11.900500 10.827750 15.115665
331 1 0.728882 5.169254 15.227356
332 1 5.489082 5.169254 15.227356
333 1 10.249282 5.169254 15.227356
334 1 4.031318 11.665904 15.227356
335 1 8.791518 11.665904 15.227356
336 1 13.551718 11.665904 15.227356
337 1 1.651218 3.003704 16.378125
338 1 6.411418 3.003704 16.378125
339 1 11.171618 3.003704 16.378125
340 1 3.108982 9.500354 16.378125
341 1 7.869182 9.500354 16.378125
342 1 12.629382 9.500354 16.378125
343 2 -0.000000 -0.000000 16.489817
344 2 4.760200 0.000000 16.489817
345 2 9.520400 0.000000 16.489817
346 2 -0.000000 3.841859 16.489817
347 2 4.760200 3.841859 16.489817
348 2 9.520400 3.841859 16.489817
349 1 3.302436 5.169254 16.489817
350 1 8.062636 5.169254 16.489817
351 1 12.822836 5.169254 16.489817
352 2 -0.000000 6.496650 16.489817
353 2 4.760200 6.496650 16.489817
354 2 9.520400 6.496650 16.489817
355 2 -0.000000 10.338509 16.489817
356 2 4.760200 10.338509 16.489817
357 2 9.520400 10.338509 16.489817
358 1 1.457764 11.665904 16.489817
359 1 6.217964 11.665904 16.489817
360 1 10.978164 11.665904 16.489817
Visualize your trajectory. What does it look like?
What is your thermo output.
The neighborlist overflow is only the symptom, the cause is more likely a bad geometry or bad potential parameters which cause the system to collapse.
FYI, I just took your data file and make a quick check with the Streitz-Mintmire potential for alumina bundled with LAMMPS and I don’t see any neighborlist overflows. The simulation cell is a little to small for this potential, but otherwise it looks fine, so I suspect that your pair style settings / potential parameters are bad.
Many thanks for looking at my data file.
May I ask you please tell me how to change them?
No change to the data file was needed.
Have you checked the potential file you are using.
Is it suitable for Al2O3? without any coulomb interactions?
Have you looked up the reference publication?
I am learning lammps and trying to find the best potential for Al2O3 in other literature or reports.
May I ask you how to check coulomb interaction?
What potential to use for your simulations and how to use LAMMPS are two very different issues.
For the former you have to study text books and the literature (and discuss with your adviser/supervisor/tutor). I (and most other people here) don’t have the time to train you in doing research. That is what advisers are for (and usually also get paid for).
I can assist with the technical issues of running LAMMPS and particular problems that are specific to LAMMPS. That said, it makes no sense to run any simulations on Al2O3 unless you have a better understanding for what to choose and where to get the parameters. Since oxides are generally more difficult to do, I suggest you do your learning of LAMMPS with a simpler system. The classic example is liquid argon with a Lennard-Jones potential. Then you can “graduate” to checking out metals or crystal/amorphous silicon with a manybody potential and testing the simulation protocols for your real research topic. Starting all of this directly without gradually building your skills is a going to be an exercise in frustration and failures. …and most importantly, this should all be done with the guidance and oversight of a suitably competent adviser/tutor. Trying to teach these skill on your own is a recipe for failure. Only true a genius can master this, and there are not many around (I am most certainly not one of them, I learned MD exactly as I described from my adviser in person).