hello.
i try to simulate a GaAs structure with some more atoms in surface, and put in run simulation.
i use this script:
Initialize
clear
units metal
dimension 3
boundary p p f
atom_style atomic
Create atoms
read_data data.GAAS_progresivo
SW Potential
pair_style sw
pair_coeff * * parametros.sw Ga As
Define Settings
#base
region r_bottom block INF INF INF INF INF 5.0 units box
group g_bottom region r_bottom
#sustrato a 49 es el original
region r_middle block INF INF INF INF 5.1 50 units box
group g_middle region r_middle
#area intermedia de 50 a 64.9
region r_deposition block INF INF INF INF 50.1 150 units box
group g_deposition region r_deposition
#parametros
velocity all create 1000 492459 rot yes dist gaussian
compute 1 all temp
fix nvt_deposition all nvt temp 300 800 0.1
fix muro all wall/reflect zhi 140 units box
fix fix_bottom g_bottom setforce 0.0 0.0 0.0
thermo 5000
Diffusion run
dump salidadump all atom 50000 dump.salidaprogresiva_2
timestep 0.005
run 500000
the structure GaAs is in the attached image.
this structure have z= 50 A, but i define the simulation box from 0 to 150, becouse i want see if some atoms fly away of surface. In this case i put the “fix muro” and try atoms not go out of simulation in z high. i try with EDGE, but also atoms go out of simulation box.
my question is:
The “fix Muro” could give the problem?, i think not run good.
someone see other cause of lose atoms in this simple simulation.
King Regards,
Bernardo
hello.
i try to simulate a GaAs structure with some more atoms in surface, and put
in run simulation.
i use this script:
# Initialize
clear
units metal
dimension 3
boundary p p f
atom_style atomic
# Create atoms
read_data data.GAAS_progresivo
# SW Potential
pair_style sw
pair_coeff * * parametros.sw Ga As
# Define Settings
#base
region r_bottom block INF INF INF INF INF 5.0 units box
group g_bottom region r_bottom
#sustrato a 49 es el original
region r_middle block INF INF INF INF 5.1 50 units box
group g_middle region r_middle
#area intermedia de 50 a 64.9
region r_deposition block INF INF INF INF 50.1 150 units box
group g_deposition region r_deposition
#parametros
velocity all create 1000 492459 rot yes dist gaussian
compute 1 all temp
fix nvt_deposition all nvt temp 300 800 0.1
fix muro all wall/reflect zhi 140 units box
fix fix_bottom g_bottom setforce 0.0 0.0 0.0
thermo 5000
# Diffusion run
dump salidadump all atom 50000 dump.salidaprogresiva_2
timestep 0.005
run 500000
the structure GaAs is in the attached image.
this structure have z= 50 A, but i define the simulation box from 0 to 150,
becouse i want see if some atoms fly away of surface. In this case i put the
"fix muro" and try atoms not go out of simulation in z high. i try with
EDGE, but also atoms go out of simulation box.
my question is:
The "fix Muro" could give the problem?, i think not run good.
someone see other cause of lose atoms in this simple simulation.
yes. the lost atoms more likely originate form atoms leaving through
the bottom of the cell.
while you are using fix setforce 0.0 0.0 0.0 on those bottom atoms,
you still assign them a velocity and time integrate them.
if you want to immobilize atoms you have to either exclude them from
time integration or assign zero velocities in addition to setting
force to zero.
axel.
hello
thank a lot i dont see that.
i think two potential solutions:
1- velocity g_bottom set 0.0 0.0 0.0
2- fix muro2 all wall/reflect zlo EDGE
which one could be better?
King Regards
Bernardo
hello.
i try to simulate a GaAs structure with some more atoms in surface, and put
in run simulation.
i use this script:
Initialize
clear
units metal
dimension 3
boundary p p f
atom_style atomic
Create atoms
read_data data.GAAS_progresivo
SW Potential
pair_style sw
pair_coeff * * parametros.sw Ga As
Define Settings
#base
region r_bottom block INF INF INF INF INF 5.0 units box
group g_bottom region r_bottom
#sustrato a 49 es el original
region r_middle block INF INF INF INF 5.1 50 units box
group g_middle region r_middle
#area intermedia de 50 a 64.9
region r_deposition block INF INF INF INF 50.1 150 units box
group g_deposition region r_deposition
#parametros
velocity all create 1000 492459 rot yes dist gaussian
compute 1 all temp
fix nvt_deposition all nvt temp 300 800 0.1
fix muro all wall/reflect zhi 140 units box
fix fix_bottom g_bottom setforce 0.0 0.0 0.0
thermo 5000
Diffusion run
dump salidadump all atom 50000 dump.salidaprogresiva_2
timestep 0.005
run 500000
the structure GaAs is in the attached image.
this structure have z= 50 A, but i define the simulation box from 0 to 150,
becouse i want see if some atoms fly away of surface. In this case i put the
“fix muro” and try atoms not go out of simulation in z high. i try with
EDGE, but also atoms go out of simulation box.
my question is:
The “fix Muro” could give the problem?, i think not run good.
someone see other cause of lose atoms in this simple simulation.
yes. the lost atoms more likely originate form atoms leaving through
the bottom of the cell.
while you are using fix setforce 0.0 0.0 0.0 on those bottom atoms,
you still assign them a velocity and time integrate them.
if you want to immobilize atoms you have to either exclude them from
time integration or assign zero velocities in addition to setting
force to zero.
axel.
hello
thank a lot i dont see that.
i think two potential solutions:
1- velocity g_bottom set 0.0 0.0 0.0
2- fix muro2 all wall/reflect zlo EDGE
which one could be better?
1
but _even better_ would in my opinion be:
group mobile all g_bottom
and then use group mobile in fix nvt instead of group all.
axel.
hello
thank a lot i dont see that.
i think two potential solutions:
1- velocity g_bottom set 0.0 0.0 0.0
2- fix muro2 all wall/reflect zlo EDGE
which one could be better?
1
but _even better_ would in my opinion be:
group mobile all g_bottom
correction:
group mobile subtract all g_bottom