Dear Lammpsers,
Actually, I think something is wrong with the set charge command.
I am trying to simulate TiO2 using Matsui & Akaogi potential with Pair_style Buck command. I inserted the required potential parameters from the paper. So. I think the pair_style and pair_coefficient commands work correct.Lattice parameters have also be rechecked with the crystallographic texts. But, the model still explode at 300K which is not expected.
Any help is highly appreciated.
Best regards,
dimension 3
units metal
atom_style charge
boundary p p p
region box block 0 4.59373 0 4.59373 0 2.95812 units box
create_box 2 box #2 is number of atoms
lattice custom 1 a1 4.59373 0.00000 0.00000 a2 0.0000 4.59373 0.00000 a3 0.00000 0.00000 2.95812 &
basis 0.0000 0.0000 0.0000 &
basis 0.5000 0.5000 0.5000 &
basis 0.3053 0.3053 0.0000 &
basis 0.6947 0.6947 0.0000 &
basis 0.8053 0.1947 0.5000 &
basis 0.1947 0.8053 0.5000 &
mass 1 47.86
mass 2 16.00
create_atoms 2 region box &
basis 1 1 &
basis 2 1 &
basis 3 2 &
basis 4 2 &
basis 5 2 &
basis 6 2
set atom 1 type 1
set atom 2 type 2
set type 1 charge 2.196
set type 2 charge -1.098
group box region box
pair_style buck/coul/long 2.5
pair_coeff 1 1 31120 0.154 5.250
pair_coeff 1 2 16958 0.194 12.590
pair_coeff 2 2 11783 0.234 30.220
kspace_style ewald 1.0e-4
fix 2 box nvt temp 300.0 300.0 100.0
#thermo_modify lost ignore flush yes
thermo 100
dump 2 box image 200 image.*.JPG type type adiam 1.0 axes yes 0.8 0.02 zoom 1.0 view 80 -30
run 2000
PS: I am using LAMMPS 32-bit 20160603 on Win.7
Dear Lammpsers,
Actually, I think something is wrong with the *set charge command.*
that is a claim which is *highly* unlikely to be true (please recall how
long LAMMPS has been around and how very unlikely it would be that such a
fundamental flow would go unnoticed) and extremely easy to prove: just use
the dump or write_dump or write_data command to output the charges with the
coordinates and atom types.
i am extremely confident, that set charge is working correctly.
[...]
set atom 1 type 1
set atom 2 type 2
what is the purpose of these two statements?? they make no sense in the
context of your input. atom types for your input are set during the
"create_atoms" command. again, have you checked if the assignment of atom
types matches the geometry? this is easily done the same way as for the
charges.
set type 1 charge 2.196
set type 2 charge -1.098
group box region box
this command makes no sense either. the group of all atoms inside the
simulation box is predefined as group "all".
axel.
You can verify a “set charge” command did what
you expect, by writing a dump file (e.g. write_dump)
and looking at the per-atom charge values.
Steve
Axel, Steve,
Thank you very much for your comment. I corrected the set commands in the input file and could finally see the atoms charge inside the dump file. I also omitted the region command.
But when I run this file at 300K, I cannot see any typical vibration at 300k! I am not sure but I think something is wrong in my file again.
any help is highly appreciated.
dimension 3
units metal
atom_style charge
boundary p p p
region box block 0 4.59373 0 4.59373 0 2.95812 units box
create_box 2 box #2 is number of atoms
lattice custom 1 a1 4.59373 0.00000 0.00000 a2 0.0000 4.59373 0.00000 a3 0.00000 0.00000 2.95812 &
basis 0.0000 0.0000 0.0000 &
basis 0.5000 0.5000 0.5000 &
basis 0.3053 0.3053 0.0000 &
basis 0.6947 0.6947 0.0000 &
basis 0.8053 0.1947 0.5000 &
basis 0.1947 0.8053 0.5000 &
mass 1 47.86
mass 2 16.00
create_atoms 2 region box &
basis 1 1 &
basis 2 1 &
basis 3 2 &
basis 4 2 &
basis 5 2 &
basis 6 2
set type 1 charge 2.196
set type 2 charge -1.098
pair_style buck/coul/long 2.5
pair_coeff 1 1 31120 0.154 5.250
pair_coeff 1 2 16958 0.194 12.590
pair_coeff 2 2 11783 0.234 30.220
kspace_style ewald 1.0e-4
fix 1 all nvt temp 300.0 300.0 100.0
thermo 100
dump 2 all image 200 image.*.JPG type type adiam 1.0 axes yes 0.8 0.02 zoom 1.0 view 80 -30
dump 3 all custom 200 dump x y z q
run 2000
Regards,
Bahman
Axel, Steve,
Thank you very much for your comment. I corrected the set commands in the
input file and could finally see the atoms charge inside the dump file. I
also omitted the region command.
But when I run this file at 300K, I cannot see any typical vibration at
300k! I am not sure but I think something is wrong in my file again.
as far as LAMMPS is concerned, your input is syntactically correct and the
simulation is doing exactly what you are asking it to do.
the remaining issues are with your various choice of MD parameters and
expectations. there are conceptual issues with your selected system size,
your non-bonded interaction cutoff, your length of trajectory, your choice
of initializing the temperature and possibly more.
to explain all of that with sufficient detail, i would have to give you a
lecture on how to do proper MD simulations, what to look for, how to choose
parameters and so on. this mailing list is not the place for it. you
should pick up a text book on MD and also talk to somebody local with MD
experience that is willing to collaborate with you, advise and oversee your
learning of MD simulations and generally look over your shoulder during
this learning phase. this is difficult to do via e-mail.
axel.
Thank you for your comment. But atually I do not think that the input file syntactically works correctly. Since, temperature
cannot fix on 300.0K and is fluctuating around 5k !
I could solve the problem. the problem is the damping factor in fix nvt command.