tabulated potential with large gradient in short range distance

Dear all,

I tried to simulate alpha quartz with a special potential proposed in this paper http://www.sciencedirect.com/science/article/pii/S0022309315301253.

I linearly tabulated potential in two ways: Firstly, I use log scale of distance (from 10^i for i=-3 to 1 by 0.0004, giving 10001 data points); Also, I considered even space in the square of distance (r^2 from 0.000001 to 99.800001 by 0.01, giving 9981 data points). I used pair_write to see how well the interpolation but for distance less than 0.1, interpolations from both setting are very bad.

The potential table is created by Mathematica with a log scale distance.

Can I ask how to improve the interpolation in short range with large gradient?

Many thanks

Bingyu Cui

#Initialization############################################################

units metal

dimension 3

boundary p p p

atom_style charge

Atom definition##########################################################

lattice custom 5.4047 &
a1 0.9092 0.0000 0.0000 &
a2 -0.4546 0.7873 0.0000 &
a3 0.0000 0.0000 1.0000 &
basis 0.4697 0.0000 0.0000 &
basis 0.0000 0.4697 0.6667 &
basis 0.5303 0.5303 0.3333 &
basis 0.4133 0.2672 0.1188 &
basis 0.2672 0.4133 0.5479 &
basis 0.7328 0.1461 0.7855 &
basis 0.5867 0.8539 0.2145 &
basis 0.8539 0.5867 0.4521 &
basis 0.1461 0.7328 0.8812

region simbox block 0 2 0 2 0 2 units lattice

create_box 2 simbox

create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2

mass 1 28.0855

mass 2 15.9994

group siliconatoms type 1

group oxygenatoms type 2

set group siliconatoms charge 2.4

set group oxygenatoms charge -1.2

Si type 1, O type 2

pair_style table linear 10001

pair_coeff 1 1 potential.table SiSi

pair_coeff 1 2 potential.table SiO

pair_coeff 2 2 potential.table OO

neigh_modify every 1 delay 0 check yes

pair_write 1 2 10001 r 0.001 10.0 table.txt Si_O 2.4 -1.2

pair_write 2 2 10001 r 0.001 10.0 table.txt O_O -1.2 -1.2

pair_write 1 1 10001 r 0.001 10.0 table.txt Si_Si 2.4 2.4

Equilibrate

fix 1 all npt temp 1986.15 5200.0 0.1 iso 1.0 1.0 1

thermo_style custom step temp pe etotal press pxx pyy pzz vol
thermo 10

dump 1 all atom 1000 dump1.qua
timestep 0.001

run 1000000

unfix 1

fix 1 all npt temp 5200.0 5200.0 0.1 iso 1.0 1.0 1

thermo_style custom step temp pe etotal press pxx pyy pzz vol
thermo 10

dump 2 all atom 1000 dump2.qua
timestep 0.001

run 10000

unfix 1

fix 1 all box/relax iso 0.0 vmax 0.001

thermo_style custom step temp pe etotal press pxx pyy pzz vol
thermo 10

dump 3 all atom 1000 dump3.qua
timestep 0.001

run 1000000

min_style cg

minimize 1e-25 1e-25 5000 10000

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Dear all,

I tried to simulate alpha quartz with a special potential proposed in this
paper http://www.sciencedirect.com/science/article/pii/S0022309315301253.

I linearly tabulated potential in two ways: Firstly, I use log scale of
distance (from 10^i for i=-3 to 1 by 0.0004, giving 10001 data points);
Also, I considered even space in the square of distance (r^2 from 0.000001
to 99.800001 by 0.01, giving 9981 data points). I used pair_write to see
how well the interpolation but for distance less than 0.1, interpolations
from both setting are very bad.

​please look up the diameter for the atoms in your system and typical or
minimal bond lengths for the conditions of your system. i'd wager a guess,
that those atoms would never come as closes as 1.0 angstrom, let alone 0.1
\AA. so, if the tabulation is only bad for such short distances, then i
would not worry.

axel.

Dear Dr. Axel,

Thank you for your quick answer. Yes, the actual atomic sizes of silicon and oxygen should prevent them from getting as close as 0.1 \AA However, when I instead interpolate tabulate potential from 10^-1 \AA, then lammps reported an error that pair distance is less than table inner cutoff. Further, when writing input script, I only set atomic mass and charge without bond nor atomic size.

How can we know short range potential (< 1\AA) will not be used?

Thanks

Bingyu Cui

Dear Dr. Axel,

Thank you for your quick answer. Yes, the actual atomic sizes of silicon
and oxygen should prevent them from getting as close as 0.1 \AA However,
when I instead interpolate tabulate potential from 10^-1 \AA, then lammps
reported an error that pair distance is less than table inner cutoff.
Further, when writing input script, I only set atomic mass and charge
without bond nor atomic size.

How can we know short range potential (< 1\AA) will not be used?

​from knowing the physics of your system.

axel.​