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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: Tue, 29 Aug 2017 18:45:26 -0400



On Tue, Aug 29, 2017 at 6:43 PM, Xiaoyu Wang <xwang181@...5819.....> 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.