I don't know what your model is. But you can use NPT to compute
the pressure with all the atoms (the only option), but only
integrate the atoms in the group. See also the dilate keyword if
you don't want some atoms (e.g. the boundary) to move when the
box dilates.
Steve
Thanks Steve,
Things seem much clearer now.You have been really helpful.
Friends,
I run the simulation again using the fix npt and when the equilibration takes place the molecules still flyoff from the surface.Any idea what is going wrong? The initial temperatures are very high. The layers fly off and then do not return to the original lattice positions. I am attaching the log files herewith.
Code:
dimension 2
units metal
boundary p p p
atom_style atomic
neighbor 3 bin
neigh_modify delay 1
lattice hex 1
region box block 0 142.1 -75 75 -0.25 0.25
create_box 5 box
mass 1 1
mass 2 1
mass 3 56
mass 4 56
mass 5 56
region lof block 0 141.1 0 1.1 INF INF
region lo-slab block 0 141.1 1.1 8.1 INF INF
create_atoms 1 region lo-slab
create_atoms 2 region lof
pair_style eam
pair_coeff * * cuu3.eam
group mobile region lo-slab
group mobile type 2
group boundary region lof
fix 2 boundary setforce 0 0 0
fix 3 mobile npt 200.0 200.0 100.0 xyz 1 1 1000.0 dilate partial
velocity all create 200.0 475367 dist gaussian
thermo 50
dump 100 all atom 1 dump.npt2
log log.npt2
run 300000
The log file starting:(detailed log file has been attached)
run 300000
Memory usage per processor = 2.6512 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 25 507283.38 0 507288.56 -232941.27 36918.663
50 9188.621 515293.62 0 517197.94 -372102.83 36918.56
100 224645.2 816537.22 0 863094.29 7833210.3 36918.597
150 268361.78 819970.19 0 875587.39 7591047.2 36923.352
200 294716.39 821041.6 0 882120.72 7277181.3 36934.29
250 313713.12 819641.59 0 884657.73 7377231.6 36951.388
300 326354.35 791908.35 0 859544.34 7104593 36974.649
350 336355.04 779525.23 0 849233.83 7244862.7 37003.895
400 350159.34 758300.3 0 830869.81 6976482.3 37039.032
450 358961.38 746672.68 0 821066.38 7195516.1 37079.979
500 367698.3 706261.63 0 782466.04 6644960 37126.774
550 381675.35 693282.95 0 772384.06 6739185.8 37179.192
600 388777.4 669646.27 0 750219.25 6618150.6 37237.258
650 401292.6 652716.83 0 735883.56 6385746.3 37300.846
700 408719.84 623508.85 0 708214.85 6188096.7 37369.855
750 421218.21 617729.76 0 705026.01 6353217.8 37444.175
800 430863.98 595591.69 0 684887 6077799.7 37523.823
…
Thanks in Advance,
Regards,
Nandu Gopan
log.npt2 (80.2 KB)
Friends,
I run the simulation again using the fix npt and when the equilibration
takes place the molecules still flyoff from the surface.Any idea what is
going wrong? The initial temperatures are very high. The layers fly off and
then do not return to the original lattice positions. I am attaching the log
so your initial configuration is of very high potential energy.
you have to find out whether this is ok or not. and either
correct your initial configuration or run a minimization first.
cheers,
axe;
There are several things wrong with your input script.
You are running a 2d problem, and not using fix enforce2d.
See the howto in the manual on running 2d simulations. You
are also using EAM potentials which are parameterized for 3d,
not 2d. The number of neighbors per atom and hence the density
functional around each atom will be way off for a 2d system.
Thus you will get bogus energies and forces.
Steve