Deposit command, not take fix nvt of structure.

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1

hello

i try to simulate a deposition of GaAs atoms in a GaAs surface, i use a GaAs sustrate, and create a enviroment where i put atoms of Ga and As.

the problem is if i created the GaAs atoms in gaas before simulation, this atoms move and are deposited in good matter, but when i use deposit command the atoms added with deposit not move (i think this atoms not move becouse i dont use vx/vz/vy parameters) but if i use this parameters all atoms could take the same direction, and i dont see the fix nvt take effect in this new atoms deposited with the command deposit, i see a new option (rate) but i dont know if this option could move the atoms in randoms directions, and take the fix nvt defined in this area.

i add the code more bellow

King Regards

Code:

Initialize

clear
units metal
dimension 3
boundary p p f
atom_style atomic

Create atoms

read_data data.GAAS

SW Potential

pair_style sw
pair_coeff * * parametros.sw Ga As

Define Settings

region r_bottom block INF INF INF INF INF 3.0 units box
group g_bottom region r_bottom
region r_middle block INF INF INF INF 3.0 49.0 units box
group g_middle region r_middle
region r_top block INF INF INF INF 65.0 INF units box
group g_top region r_top
region r_deposition block INF INF INF INF 50.9 64.9 units box
group g_deposition region r_deposition
region r_gas block INF INF INF INF 65.0 INF units box
group g_gas region r_gas
region depo block 5.0 97.0 5.0 97.0 70.0 215.0
#parametros
velocity g_gas create 1000 492459 rot yes dist gaussian
fix nve_deposition g_deposition nve
fix fix_bottom g_bottom setforce 0.0 0.0 0.0
fix nvt_middle g_middle nvt temp 600 800 0.1
fix nvt_gas g_gas nvt temp 1000 1200 0.1
fix muro all wall/reflect zhi EDGE
thermo 5000
thermo_modify lost ignore
dump salidadump all atom 20000 dump.salidagaas
timestep 0.001
run 600000

minimize 1.0e-4 1.0e-6 1000 10000
fix 6 all deposit 300 1 10 67546 region depo near 4.2 units box
fix 7 all deposit 300 2 10 69546 region depo near 4.2 units box

run 600000
dump dumpfinal all atom 100000 dump.final
minimize 1.0e-4 1.0e-6 1000 10000

2

The fix deposit command allows you to specify a range of velocities

for new atoms, in x,y, and/or z. The actual velocity of one atom

will be chosen randomly from those ranges. You probably don’t want

the thermostat to apply to the new atoms, at least not immediately.

I suggest you use fix langevin on the substrate atoms.

Steve

3

hello

i try to simulate a deposition of GaAs atoms in a GaAs surface, i use a GaAs
sustrate, and create a enviroment where i put atoms of Ga and As.

the problem is if i created the GaAs atoms in gaas before simulation, this
atoms move and are deposited in good matter, but when i use deposit command
the atoms added with deposit not move (i think this atoms not move becouse i
dont use vx/vz/vy parameters) but if i use this parameters all atoms could

no. your deposited atoms do not move because they are not time integrated.
in your input to apply time integration to groups:
g_deposition, g_middle and g_gas

however, you do not add your deposited atoms to any of those groups.
only to group all.

axel.

4

hello

i add the deposit to group and add one fix nvt but atoms continue without move.

i add lines with *** , but nothing happend in simulacion.
thank alot.

CODE:

Initialize

clear
units metal
dimension 3
boundary p p f
atom_style atomic

Create atoms

read_data data.GAAS

SW Potential

pair_style sw
pair_coeff * * parametros.sw Ga As

Define Settings

region r_bottom block INF INF INF INF INF 3.0 units box
group g_bottom region r_bottom
region r_middle block INF INF INF INF 3.0 49.0 units box
group g_middle region r_middle
region r_top block INF INF INF INF 65.0 INF units box
group g_top region r_top
region r_deposition block INF INF INF INF 50.9 64.9 units box
group g_deposition region r_deposition
region r_gas block INF INF INF INF 65.0 INF units box
group g_gas region r_gas
region depo block 5.0 97.0 5.0 97.0 70.0 215.0
group g_gas_d region depo ***

#parametros
velocity g_gas create 1000 492459 rot yes dist gaussian

fix nve_deposition g_deposition nve
fix fix_bottom g_bottom setforce 0.0 0.0 0.0
#fix nvt_deposition g_deposition nvt temp 600 800 0.1
#fix nvt_middle g_middle nve
fix nvt_middle g_middle nvt temp 600 800 0.1
fix nvt_gas g_gas nvt temp 1000 1200 0.1
fix nvt_gas_d g_gas_d nvt temp 1000 1200 0.1 ***
fix muro all wall/reflect zhi EDGE

thermo 5000
#thermo_style custom step temp pe etotal

thermo_modify lost ignore

Diffusion run

dump salidadump all atom 20000 dump.salidagaas
#si el paso es mas grade da NaN (0.05 fallaba).
timestep 0.001

#dump dumpfinal all atom 100000 dump.final
#restart 100000 deposicion.restart
run 600000

minimize 1.0e-4 1.0e-6 1000 10000
#los valores de gaas depositados con estos parametros no se mueven.
fix 6 all deposit 300 1 10 67546 region depo near 4.2 units box

fix 7 all deposit 300 2 10 69546 region depo near 4.2 units box

run 600000
dump dumpfinal all atom 100000 dump.final
minimize 1.0e-4 1.0e-6 1000 10000

hello

i try to simulate a deposition of GaAs atoms in a GaAs surface, i use a GaAs
sustrate, and create a enviroment where i put atoms of Ga and As.

the problem is if i created the GaAs atoms in gaas before simulation, this
atoms move and are deposited in good matter, but when i use deposit command
the atoms added with deposit not move (i think this atoms not move becouse i
dont use vx/vz/vy parameters) but if i use this parameters all atoms could

no. your deposited atoms do not move because they are not time integrated.
in your input to apply time integration to groups:
g_deposition, g_middle and g_gas

however, you do not add your deposited atoms to any of those groups.
only to group all.

axel.