Hi all:
I am trying to run a NPT simulation on cubic ZrO2 containing Y2O3 as
dopants. My input file is:
units metal
atom_style charge
atom_modify map array sort 0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
boundary p p p
read_restart restart.8YTZP.bulk
#Potential
pair_style buck/coul/long 4.0 10.0
pair_modify shift yes
pair_coeff 1 1 0.0 10.0 0.0
pair_coeff 2 2 9547.96 0.2192 32.0 # Minervini
pair_coeff 3 3 0.0 10.0 0.0
pair_coeff 1 2 1502.11 0.3477 5.1 # Idem
pair_coeff 1 3 0.0 10.0 0.0
pair_coeff 2 3 1766.40 0.33849 19.43
kspace_style ewald 1.0e-4
velocity all create 300.0 82986 dist gaussian mom no
#Output settings
thermo_style custom step temp etotal press vol
thermo 50
thermo_modify lost warn norm yes
#Molecular Dynamics settings
fix 3 all press/berendsen iso 31300.0 31300.0 0.5
fix 4 all temp/berendsen 300.0 300.0 0.5
fix 5 all npt temp 300.0 300.0 0.1 iso 31300.0 31300.0 0.1 nreset 10 drag
1.0
dump 1 all cfg 100 dump.cfg.* id type xs ys zs q
dump_modify 1 element Zr O Y
dump 2 all custom 1 dump.prueba id type q x y z
run 10000
Data are read from a previous minimization carried out at 0 K. When I
launch the job I get the following output:
LAMMPS (26 Apr 2010)
Reading restart file ...
orthogonal box = (-10.258 -10.258 -25.645) to (10.258 10.258 25.645)
1 by 1 by 2 processor grid
1873 atoms
Ewald initialization ...
G vector = 0.273155
vectors: actual 1d max = 845 13 9841
Setting up run ...
Memory usage per processor = 5.25492 Mbytes
Step Temp TotEng Press Volume
431 300 -35.73188 34867.455 21588.282
450 nan nan nan nan
500 nan nan nan nan
and so on. This does not happen when I use temp/Berendsen + npt alone, but
only when I use press/Berendsen.
Any idea about what is going on here?
Thanks in advance!
Juanjo
2010/5/4 Juan J. Meléndez Martínez <melendez@…12…1779…>
Hi all:
I am trying to run a NPT simulation on cubic ZrO2 containing Y2O3 as
dopants. My input file is:
units metal
atom_style charge
atom_modify map array sort 0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
boundary p p p
read_restart restart.8YTZP.bulk
#Potential
pair_style buck/coul/long 4.0 10.0
pair_modify shift yes
pair_coeff 1 1 0.0 10.0 0.0
pair_coeff 2 2 9547.96 0.2192 32.0 # Minervini
pair_coeff 3 3 0.0 10.0 0.0
pair_coeff 1 2 1502.11 0.3477 5.1 # Idem
pair_coeff 1 3 0.0 10.0 0.0
pair_coeff 2 3 1766.40 0.33849 19.43
kspace_style ewald 1.0e-4
velocity all create 300.0 82986 dist gaussian mom no
#Output settings
thermo_style custom step temp etotal press vol
thermo 50
thermo_modify lost warn norm yes
#Molecular Dynamics settings
fix 3 all press/berendsen iso 31300.0 31300.0 0.5
fix 4 all temp/berendsen 300.0 300.0 0.5
fix 5 all npt temp 300.0 300.0 0.1 iso 31300.0 31300.0 0.1 nreset 10 drag
1.0
dump 1 all cfg 100 dump.cfg.* id type xs ys zs q
dump_modify 1 element Zr O Y
dump 2 all custom 1 dump.prueba id type q x y z
run 10000
Data are read from a previous minimization carried out at 0 K. When I
launch the job I get the following output:
LAMMPS (26 Apr 2010)
Reading restart file …
orthogonal box = (-10.258 -10.258 -25.645) to (10.258 10.258 25.645)
1 by 1 by 2 processor grid
1873 atoms
Ewald initialization …
G vector = 0.273155
vectors: actual 1d max = 845 13 9841
Setting up run …
Memory usage per processor = 5.25492 Mbytes
Step Temp TotEng Press Volume
431 300 -35.73188 34867.455 21588.282
450 nan nan nan nan
500 nan nan nan nan
and so on. This does not happen when I use temp/Berendsen + npt alone, but
only when I use press/Berendsen.
Any idea about what is going on here?
Well, for starters, you shouldn’t be combining either temp/berendsen or press/berendsen with fix npt, which already includes a barostat and a thermostat. If you’re using temp/berendsen or press/berendsen, you should probably be using something like fix nve instead. . . .
–AEI
Try printing thermo info every step using multi command. See whether this occurs at the very first step or after few steps. Also, observe which contribution of the energy is blowing up to NAN. that could give you some insights.
2010/5/4 Juan J. Meléndez Martínez <melendez@…1779…>
Ahmed is correct - you are using 2 thermostats
and 2 barostats.
Steve
2010/5/4 Ahmed E. Ismail <[email protected]...>: