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Re: [lammps-users] energetic Au deposition into polymer
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Re: [lammps-users] energetic Au deposition into polymer


From: Fernanda S Teixeira <nandast@...6816...>
Date: Wed, 21 Jun 2017 10:59:33 -0300

Dear all,

  I think I got what is happening. The bond is broken by fix bond/break and one of the atoms are sputtered from the surface and that is normal for deposition. So I have used 

"thermo_modify temp all lost ignore lost/bond ignore flush yes" to ignore those atoms.

  The atom is gone but I got now the error:

ERROR: Fix bond/break needs ghost atoms from further away (../fix_bond_break.cpp:406)
*** Error in `lmp_g++': double free or corruption (!prev): 0x0000000003569460 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7364f)[0x7f01fe64c64f]
/lib64/libc.so.6(+0x78eae)[0x7f01fe651eae]
/lib64/libc.so.6(+0x79b87)[0x7f01fe652b87]
lmp_g++(_ZN9LAMMPS_NS6ThermoD1Ev+0x34)[0xa66404]
lmp_g++(_ZN9LAMMPS_NS6ThermoD0Ev+0x9)[0xa66479]
lmp_g++(_ZN9LAMMPS_NS6OutputD2Ev+0x27)[0x1252e07]
etc...
.
.
Aborted

Fernanda S Teixeira



Em Ter, 2017-06-20 às 13:58 -0300, Fernanda S Teixeira escreveu:
Dear all,

   My substrate are coarse-grained PMMA. The monomers from the same chain are are linked by FENE bonds and monomers from different chains interact via LJ. The system was equilibrated. The correspondent data file is attached ("pmma_final.dat"). I am depositing energetic atoms of Au. I divided the deposition regions into 16 different areas, so I have 1 particle deposited for a square nanometer. My script is bellow.
   I am playing with langevin damping parameter and I am also using fix bond/break to simulate polymer damage.  I am doing deposition in loops, so I can run nvt and also force bias monte carlo between deposition events. 

   When I use a damping parameters that does not break bonds (0.01), everything is ok. But when I use values higher than 0.02 and some bonds are broken (for my criteria, typically 2-3 broke bonds per deposition), I got this kind of message (after 2 or 3 loops):

ERROR on proc 0: Bond atoms 208 209 missing on proc 0 at step 511010 (../neigh_bond.cpp:65)


Sometimes it happens just after deposition, sometimes during monte nvt or fb monte carlo.

This happens for 1 or more processors.
Maybe is bad dynamics, but I tracking thermo I cannot see any abrupt variation of temperature. And I tried also to increase number of steps for nvt and for fb-monte carlo.
  I have also extended communication between atoms using a larger cutoff "comm_modify cutoff 120.0"

  I would appreciated some tip.

Fernanda S Teixeira.


# Gold deposition

clear
units metal
dimension 3
boundary p p m
neighbor 2.0 bin
atom_style bond
special_bonds   fene
atom_modify map array
bond_style      fene

pair_style lj/cut 12


timestep 0.001

# ---------- Define Settings ---------------------


read_data pmma_final.dat

pair_coeff 1 1 0.07 5.16 12
pair_coeff 2 2 0.2294 2.629 12
pair_modify shift yes mix geometric



# ---------- Define Interatomic Potential ---------------------

mass 2 197.0

bond_coeff 1 0.08 7.5 0.07 5.16


# Potential Simples de Lennard-Jones

neigh_modify every 1 delay 1 check yes



thermo 500
thermo_style custom step atoms pe ke etotal lx ly lz vol temp press zlo zhi density
compute all all temp
thermo_modify temp all lost ignore flush yes


#----------------------------------------------------------------------------------
change_box all boundary p p f x final 0 40 y final 0 40 z final 0 115 #remap
#neigh_modify    delay 0
group addatoms type 2
region          mobile block 0 40 0 40 10 INF
group mobile region mobile
comm_modify cutoff 120.0



#----------------------------Running PMMA in nvt for a while



print "Equilibrando a 300 K apos mudanca na caixa"

fix nvt1 mobile nve
fix langv1 mobile langevin 300 300 0.02 587283

 
dump equilibracao_300K all xyz 1000 checagem_PMMA_mudanca_caixa.xyz

run 10000
undump equilibracao_300K
unfix nvt1
unfix langv1

#------------------------------------------------------------------------------------
# Deposition



region slab1 block 0 10 0 10 113 115
region slab2 block 0 10 10 20 113 115
region slab3 block 0 10 20 30 113 115
region slab4 block 0 10 30 40 113 115
region slab5 block 10 20 0 10 113 115
region slab6 block 10 20 10 20 113 115
region slab7 block 10 20 20 30 113 115
region slab8 block 10 20 30 40 113 115
region slab9 block 20 30 0 10 113 115
region slab10 block 20 30 10 20 113 115
region slab11 block 20 30 20 30 113 115
region slab12 block 20 30 30 40 113 115
region slab13 block 30 40 0 10 113 115
region slab14 block 30 40 10 20 113 115
region slab15 block 30 40 20 30 113 115
region slab16 block 30 40 30 40 113 115


fix bb mobile bond/break 1 1 7.5 prob 0.3 49829
thermo_style custom step atoms pe ke etotal lx ly lz vol temp press zlo zhi density f_bb[2]
thermo_modify temp all lost ignore flush yes

variable j loop 50
label loop_inicio


fix 2 addatoms nve
fix 3 mobile langevin 300.0 300.0 0.02 587283
fix 3_a mobile nve


print "Deposicao"



fix 1a addatoms deposit 1 2 100000 12345 region slab1 near 1.0 vz -140 -140
fix 2a addatoms deposit 1 2 100000 12345 region slab2 near 1.0 vz -140 -140
fix 3a addatoms deposit 1 2 100000 12345 region slab3 near 1.0 vz -140 -140
fix 4a addatoms deposit 1 2 100000 12345 region slab4 near 1.0 vz -140 -140
fix 5a addatoms deposit 1 2 100000 12345 region slab5 near 1.0 vz -140 -140
fix 6a addatoms deposit 1 2 100000 12345 region slab6 near 1.0 vz -140 -140
fix 7a addatoms deposit 1 2 100000 12345 region slab7 near 1.0 vz -140 -140
fix 8a addatoms deposit 1 2 100000 12345 region slab8 near 1.0 vz -140 -140
fix 9a addatoms deposit 1 2 100000 12345 region slab9 near 1.0 vz -140 -140
fix 10a addatoms deposit 1 2 100000 12345 region slab10 near 1.0 vz -140 -140
fix 11a addatoms deposit 1 2 100000 12345 region slab11 near 1.0 vz -140 -140
fix 12a addatoms deposit 1 2 100000 12345 region slab12 near 1.0 vz -140 -140
fix 13a addatoms deposit 1 2 100000 12345 region slab13 near 1.0 vz -140 -140
fix 14a addatoms deposit 1 2 100000 12345 region slab14 near 1.0 vz -140 -140
fix 15a addatoms deposit 1 2 100000 12345 region slab15 near 1.0 vz -140 -140
fix 16a addatoms deposit 1 2 100000 12345 region slab16 near 1.0 vz -140 -140
#fix 16a addatoms deposit 1 2 100000 12345 region slab16 near 1.0 vz -140 -140


 

dump            2a all xyz 10 PMMA_deposit_$j.xyz 


run 100000
unfix 2
unfix 3
unfix 3_a
undump 2a


#----------------------Running system in nvt for while --------------------


print "Running nvt at 300 K"

fix nvt1 mobile nve
fix nvt2 addatoms nve
fix langv1 mobile langevin 300 300 0.008 587283

run 200000

unfix nvt1
unfix nvt2
unfix langv1


#----------------------Running system in force bias MC --------------------
print "Monte Carlo"
fix mc1 mobile tfmc 0.10 300 159345 com 1 1 0 rot
fix mc2 addatoms tfmc 0.10 300 159345 com 1 1 0 rot



dump            3a all xyz 10000 PMMA_MC_$j.xyz 

run 200000
unfix mc1
unfix mc2
undump 3a


next j
jump Loop_PMMA_deposit_op.in loop_inicio

write_data deposition.dat

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--
Dra. Fernanda de Sá Teixeira
Especialista em Laboratório
Laboratório de Filmes Finos
(http://fap.if.usp.br/~lff)
Instituto de Física da USP
Fone/Fax: 11 3091 6625 / 11 3091 7140