Dear all,
I want to get equilibrated lattice constants of crystal SiO2 at room temperature. I have searched many previous posts but I am still not clear on the procedure to control temperature and atmosphere. The total number of atoms in simulation box is 13500.
I firstly run 1000 for quick test. The problem occurs when I fix pressure since I want to relax the structure after the system is in 1 atom. At step 1000, temperature is 297, Potential is -205457, total energy is -204938 and pressure is 28496.
Then at step 1100,
Temp=297, potential energy=0, total energy=519 while pressure, volume and density all becomes -nan
I also tried to fix pressure at 1atom before fixing temperature, but then it reported: ORTE_ERROR_LOG:Data unpack would read past end of buffer in file unti/show_help.c at line 500
Why does it happen and how to fix the temperature before relaxation the structure?
Thanks
Bingyu Cui
Here is my script:
#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 0.0 10.0 0.0 10.0 0.0 10.0 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
#kspace_style pppm 1.0e-4
neigh_modify every 1 delay 0 check yes
pair_write 1 2 9999 r 0.001 10.0 table.txt Si_O 2.4 -1.2
pair_write 2 2 9999 r 0.001 10.0 table.txt O_O -1.2 -1.2
pair_write 1 1 9999 r 0.001 10.0 table.txt Si_Si 2.4 2.4
Equilibrate
velocity all create 298.15 635845 dist gaussian
fix 0 all npt temp 298.15 298.15 0.1 iso 1.01325 1.01325 1.0
unfix 0
fix 1 all nve
fix 2 all langevin 298.15 298.15 0.1 48279
thermo_style custom step temp pe etotal press vol density xlat ylat zlat
thermo 100
dump 2 all atom 1000 dump2.qua
run 1000000
unfix 1
unfix 2
fix 3 all pressure/berendsen iso 1.03125 1.03125 1.0
thermo_style custom step temp pe etotal press vol density xlat ylat zlat
thermo 100
dump 3 all atom 1000 dump3.qua
run 1000000
unfix 3
fix 4 all box/relax iso 0.0 vmax 0.001