[lammps-users] positive value of energy and nan in rdf file

Dear All,

I simulated amophous formation of SiO using ReaxFF. Radial Distribution Funtion was also calculated by writing in input file :
fix rdfcalculation all rdf 10 rdf.out 100 1 1 1 2 2 1 2 2 . .

In output file I found only 1-1 (Si-Si) has value while others are not. It looks like:

r, g(1,1,r), ncoord(1,1,r), g(1,2,r), ncoord(1,2,r), g(2,1,r), ncoord(2,1,r), g(2,2,r), ncoord(2,2,r)
0.050000 0.000000 0.000000 nan nan nan nan nan nan
0.150000 0.000000 0.000000 nan nan nan nan nan nan
0.250000 0.000000 0.000000 nan nan nan nan nan nan
0.350000 0.000000 0.000000 nan nan nan nan nan nan
0.450000 0.000000 0.000000 nan nan nan nan nan nan
0.550000 0.000000 0.000000 nan nan nan nan nan nan
0.650000 0.000000 0.000000 nan nan nan nan nan nan
0.750000 0.000000 0.000000 nan nan nan nan nan nan
0.850000 0.000000 0.000000 nan nan nan nan nan nan
0.950000 0.000000 0.000000 nan nan nan nan nan nan

from where probably the errors come from?

Other problem is within several steps, energy both total energy and potential energy are positive. Is it serious problem? what are ussually the causes?

here is my input file:

units real
boundary p p p
atom_style charge

lattice custom 5.12 a1 0.5000 -0.8666 0.0000 a2 0.5000 0.8666 0.0000 a3 0.0000 0.0000 1.1 basis 0.46990000 0.00000000 0.66666667 basis 0.00000000 0.46990000 0.33333333 basis 0.5301 0.5301 0.00000000

region mybox block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 2 mybox
create_atoms 1 region mybox basis 1 1 basis 2 1 basis 3 1

lattice custom 5.12 a1 0.5000 -0.8666 0.0000 a2 0.5000 0.8666 0.0000 a3 0.0000 0.0000 1.1 basis 0.41410000 0.26810000 0.78540000 basis 0.7319 0.14600000 0.45206667 basis 0.854 0.5859 0.11873333 basis 0.26810000 0.41410000 0.2146 basis 0.5859 0.854 0.88126667 basis 0.14600000 0.7319 0.54793333

pair_style reax 10.0 1.0e-6
pair_coeff * * ffield.reax 3 6

mass 1 15.9994
mass 2 28.086
fix rdfcalculation all rdf 10 rdf.out 100 1 1 1 2 2 1 2 2

fix 1 all temp/rescale 1 300.0 2000.0 1.05 1.0
fix 2 all nve

thermo 1
thermo_style custom step pe etotal temp press

dump annealling all custom 10 anneal_*.dat id type x y z q

timestep 0.02
run 200000

undump annealling
unfix 1
unfix 2
fix makeequilibrium all nvt 2000 2000 100

dump equlibrationhightemp all custom 10 equlibrationhightemp__*.dat id type x y z q
timestep 1
run 58000
undump equlibrationhightemp
unfix makeequilibrium

fix 3 all temp/rescale 1 2000 300.0 1.0 1.0
fix 4 all nve
dump cooling all custom 10 cool_*.dat id type x y z q
timestep 0.02
run 217950
unfix 3
unfix 4

fix secondequilibrium all nvt 300 300 100

undump cooling

dump equlibrationroomtemp all custom 10 equalroom_*.dat id type x y z q
run 20500
timestep 1

thank you,

with best wishes,

create_atoms 1 region mybox basis 1 1 basis 2 1 basis 3 1

This command will not create any atoms of type 2, which
is probably causing you problems. I'll have to look at
why the RDF command is printing NaNs, but undoubtably
you don't have a SiO model.

Steve