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Re: [lammps-users] tabulated potential with large gradient in short range distance
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Re: [lammps-users] tabulated potential with large gradient in short range distance


From: Bingyu Cui <hwtray@...8...>
Date: Sat, 4 Nov 2017 10:28:45 +0000

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

 


From: Axel Kohlmeyer <akohlmey@...24...>
Sent: Friday, November 3, 2017 9:58:04 PM
To: Bingyu Cui
Cc: lammps-users@lists.sourceforge.net
Subject: Re: [lammps-users] tabulated potential with large gradient in short range distance
 


On Fri, Nov 3, 2017 at 2:23 PM, Bingyu Cui <hwtray@...8...> wrote:

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.


 

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



# Atoms interactions settings##################################


# 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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--
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.