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Re: [lammps-users] NaN when using Qeq package
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Re: [lammps-users] NaN when using Qeq package


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 30 Aug 2017 13:30:19 -0400



On Wed, Aug 30, 2017 at 1:05 PM, Xiaoyu Wang <xwang181@...5818...> wrote:
I have used the topo to check with the data file. But I did not find overlapping in the geometry. What I am wondering is that no matter how bad the potential is, there should be an energy output. But here, only nan left.

​look at the number of entries: you have 83 atoms, but your compound is Bi_2O_3 (i.e. 5 atoms per units). that *cannot* be correct, when assuming that you want to model a bulk crystal with no defects. also, have you checked overlaps through periodic boundaries?​

this simple input will show you how many overlaps there are:

units real
atom_style charge
boundary p p p
read_data bi2o3.data

pair_style zero 5.0
pair_coeff * *

delete_atoms overlap 0.01 all all
write_data bi2o3-new.data


if you look at the output, you'll see:

Deleted 44 atoms, new total = 39

that means the delete_atoms command identifies not just a few but 44(!) atoms that are within less than 0.01 angstrom of each other.
it also looks as if one position is missing, since the remaining 39 atoms is as unreasonable as 83 (not divisible by 5) for a bulk system.

axel.
 

The following is the data file.

83 atoms
2 atom types

-1.363 6.813 xlo xhi
-1.363 6.813 ylo yhi
-1.363 6.813 zlo zhi

Masses

1 209
2 16

Atoms

1 2 -2 1.363 4.088 4.088
2 1 2.486486486 0 0 0
3 2 -2 1.363 4.088 6.813
4 1 2.486486486 5.45 2.725 2.725
5 2 -2 1.363 -1.363 4.088
6 1 2.486486486 2.725 2.725 0
7 2 -2 6.813 4.088 6.813
8 1 2.486486486 2.725 5.45 2.725
9 2 -2 1.363 -1.363 -1.363
10 1 2.486486486 0 2.725 2.725
11 2 -2 1.363 4.088 1.363
12 1 2.486486486 5.45 5.45 5.45
13 2 -2 1.363 4.088 -1.363
14 1 2.486486486 2.725 0 2.725
15 2 -2 6.813 4.088 1.363
16 1 2.486486486 2.725 2.725 5.45
17 2 -2 4.088 1.363 4.088
18 2 -2 6.813 1.363 4.088
19 2 -2 4.088 1.363 -1.363
20 2 -2 6.813 6.813 4.088
21 2 -2 -1.363 1.363 -1.363
22 2 -2 1.363 1.363 4.088
23 2 -2 -1.363 1.363 4.088
24 2 -2 1.363 6.813 4.088
25 2 -2 4.088 4.088 1.363
26 2 -2 4.088 6.813 1.363
27 2 -2 -1.363 4.088 1.363
28 2 -2 4.088 6.813 6.813
29 2 -2 -1.363 -1.363 1.363
30 2 -2 4.088 1.363 1.363
31 2 -2 4.088 -1.363 1.363
32 2 -2 4.088 1.363 6.813
33 1 2.486486486 2.725 2.725 2.725
34 2 -2 1.363 4.088 4.088
35 1 2.486486486 2.725 5.45 0
36 2 -2 1.363 4.088 1.363
37 1 2.486486486 0 5.45 2.725
38 2 -2 1.363 4.088 4.088
39 1 2.486486486 0 2.725 0
40 2 -2 1.363 4.088 1.363
41 1 2.486486486 2.725 5.45 5.45
42 2 -2 1.363 4.088 4.088
43 1 2.486486486 2.725 2.725 2.725
44 2 -2 1.363 4.088 1.363
45 1 2.486486486 0 2.725 5.45
46 2 -2 1.363 4.088 4.088
47 1 2.486486486 0 5.45 2.725
48 2 -2 1.363 4.088 1.363
49 1 2.486486486 2.725 2.725 2.725
50 2 -2 4.088 1.363 4.088
51 1 2.486486486 0 2.725 5.45
52 2 -2 1.363 1.363 4.088
53 1 2.486486486 2.725 0 5.45
54 2 -2 4.088 1.363 4.088
55 1 2.486486486 0 0 2.725
56 2 -2 1.363 1.363 4.088
57 1 2.486486486 5.45 2.725 5.45
58 2 -2 4.088 1.363 4.088
59 1 2.486486486 2.725 2.725 2.725
60 2 -2 1.363 1.363 4.088
61 1 2.486486486 5.45 0 2.725
62 2 -2 4.088 1.363 4.088
63 1 2.486486486 2.725 0 5.45
64 2 -2 1.363 1.363 4.088
65 1 2.486486486 2.725 2.725 2.725
66 2 -2 4.088 4.088 1.363
67 1 2.486486486 5.45 0 2.725
68 2 -2 4.088 1.363 1.363
69 1 2.486486486 5.45 2.725 0
70 1 2.486486486 2.725 0 0
71 1 2.486486486 5.45 5.45 2.725
72 1 2.486486486 2.725 5.45 0
73 1 2.486486486 2.725 0 5.45
74 2 -2 4.088 1.363 4.088
75 1 2.486486486 5.45 2.725 5.45
76 2 -2 1.363 4.088 1.363
77 1 2.486486486 0 2.725 0
78 1 2.486486486 0 5.45 2.725
79 2 -2 1.363 1.363 4.088
80 2 -2 1.363 4.088 4.088
81 1 2.486486486 0 2.725 5.45
82 1 2.486486486 2.725 5.45 5.45
83 1 2.486486486 0 0 2.725


On Aug 29, 2017, at 5:45 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:



On Tue, Aug 29, 2017 at 6:43 PM, Xiaoyu Wang <xwang181@...5818...> wrote:
I removed the Qeq part. But it still cannot calculate the potential energy and left as -nan in the output.

​that means, that most likely your input geometry in the data file is bogus, e.g. due to atoms overlapping atoms.

axel.

 

On Aug 29, 2017, at 5:33 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:



On Tue, Aug 29, 2017 at 6:14 PM, Xiaoyu Wang <xwang181@...5818...> wrote:
Dear all,

I was trying to develop charges on a crystal by using Qeq. I found the ionization potential and electron affinity parameters to get the Mulliken electronegativity, which is used by Qeq. But it gave NaN on charges and those energies. The crystal structure is from the standard database. It seems there is something wrong blowing up the system. Can anyone know how to deal with it? I was using the same method successfully once before, but I have no idea why this time it is not working. 

​what happens, if you run that input withOUT fix qeq and just assign fixed charges​ to some small initial guess value? do you still get NaNs?

​axel.​

 

Here is the input.

units metal
dimension 3
#boundary p p p
atom_style charge
read_data bi2o3_qeq.data

pair_style buck/coul/long 12.0
kspace_style ewald 1.0e-6

pair_coeff 1 1 6452.86 0.5089 0.0000
pair_coeff 1 2 6048.95 0.5162 0.0000
pair_coeff 2 2 5670.33 0.5235 8.1163

neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes

group           type1 type 1
compute         charge1 type1 property/atom q
compute         q1 type1 reduce ave c_charge1
group           type2 type 2
compute         charge2 type2 property/atom q
compute         q2 type2 reduce ave c_charge2
variable        qtot equal count(type1)*c_q1+count(type2)*c_q2

thermo_style    custom step pe c_q1 c_q2 v_qtot spcpu
thermo          10

timestep        0.0001

velocity        all create 300.0 1281937 
fix 1 all nve
fix 2 all qeq/dynamic 1 10 1.0e-3 100 bi2o3.parm

run 100

write_data bi2o3_qeq_o.data


Here is the error:
WARNING: Charges did not converge at step 0: nan (../fix_qeq_dynamic.cpp:165)
ERROR on proc 0: Non-numeric atom coords - simulation unstable (../domain.cpp:521)

Best wishes

Shaw

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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.




-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.




--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.