fix deposit & delete atoms

hi
   I am trying to do a deposition simulation. The process seems to stagnate due to "vapor" atoms that haven't adhered to the substrate and are flying away in the shrink-wrapped box. So I periodically delete atoms above a certain height - unfortunately the next step after the deletion (for any deletion) results in

....
  unfix DEPOSIT
  delete_atoms region DELETE
Deleted 4 atoms, new total = 248
  next i
jump SELF loop_i
  fix DEPOSIT Au deposit 168 2 20000 31456 region UP vx -0.01 0.01 vz -0.02 -0.01 local 0.1 2.0 1.0
  run 600000
Memory usage per processor = 5.45673 Mbytes
Step CPU Atoms c TotEng Temp Zlo Zhi
ERROR: Lost atoms: original 248 current 205 (thermo.cpp:385)

I've visualized the simulation and there is no atoms in the region where the atoms are deleted that are close to the accumulating substrate.

I'll also looked through the manual to see if deposit and delete are deadly combo.

anyone see this before or have a way around it?
thanks,
Reese

hi
  I am trying to do a deposition simulation. The process seems to stagnate due to "vapor" atoms that haven't adhered to the substrate and are flying away in the shrink-wrapped box. So I periodically delete atoms above a certain height - unfortunately the next step after the deletion (for any deletion) results in

....
unfix DEPOSIT
delete_atoms region DELETE
Deleted 4 atoms, new total = 248
next i
jump SELF loop_i
fix DEPOSIT Au deposit 168 2 20000 31456 region UP vx -0.01 0.01 vz -0.02 -0.01 local 0.1 2.0 1.0
run 600000
Memory usage per processor = 5.45673 Mbytes
Step CPU Atoms c TotEng Temp Zlo Zhi
ERROR: Lost atoms: original 248 current 205 (thermo.cpp:385)

I've visualized the simulation and there is no atoms in the region where the atoms are deleted that are close to the accumulating substrate.

I'll also looked through the manual to see if deposit and delete are deadly combo.

anyone see this before or have a way around it?

Yes. This happens because of the shrink-wrap boundaries suddenly
shrinking a lot. Thus when updating the domains, they are so different
that atoms appear to have moved a lot an thus are lost. People usually
use either a reflecting wall or fixed boundaries while ignoring lost
atoms.

Axel