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[lammps-users] atom deposition_segmentation fault (core dumped)
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[lammps-users] atom deposition_segmentation fault (core dumped)


From: "Gaoyang" <582660199@...1204...>
Date: Fri, 23 Jun 2017 12:15:09 +0800

Hello everyone!
I want to simulation the process of Ag atoms depositing onto ZnO substrate.
I used the commands of "fix deposit" or "velocity" to control Ag atom to deposit. But in the atoms depostion, "segmentation fault (core dumped)" appears in output screen, and the program stoped. I used to change the timestep and depositing velocity, but it cannot sovle the problem.

This is my log file.
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
LAMMPS (31 Mar 2017)
# MD simulation of depositing Ag on to ZnO substrate

# Initialization
units             real
atom_style        charge
dimension         3
newton            on
boundary          p   f   p
# structure construction
read_data       ZnOsub_y_axis.lammps
  triclinic box = (0 0 0) to (48.739 48.7391 52.0544) with tilt (0 0 0)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  3600 atoms
pair_style        reax/c lmp_control
pair_coeff        * * ffield.reax.new Zn O Ag
Reading potential file ffield.reax.new with DATE: 2011-02-18


fix               0 all nve
fix               12 all qeq/reax 1 0.0 10.0 1e-6 reax/c

#wall region

region wall block INF INF 0 10 INF INF units box
group wall region wall
1800 atoms in group wall

#moving group of atoms

group            moving subtract all wall
1800 atoms in group moving

#thermal group of atoms

region thermal block INF INF 10 20 INF INF
group thermal region thermal
1800 atoms in group thermal

#thermalise whole system

velocity          moving create 600 8882882 dist gaussian
fix               2 moving temp/berendsen 300 300 100
run 30 post no
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 9 9 9
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair reax/c, perpetual
      attributes: half, newton off, ghost
      pair build: half/bin/newtoff/ghost
      stencil: half/ghost/bin/3d/newtoff
      bin: standard
  (2) fix qeq/reax, perpetual, copy from (1)
      attributes: half, newton off, ghost
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 177.6 | 177.6 | 177.6 Mbytes
Step Temp E_pair E_mol TotEng Press
       0    299.91664   -236052.16            0   -232834.68    25273.697
      30     2564.783   -264015.07            0   -236500.25   -69879.598
Loop time of 11.9774 on 1 procs for 30 steps with 3600 atoms

96.8% CPU use with 1 MPI tasks x no OpenMP threads
unfix             2

#thermalise thermal atoms only
fix               4 moving temp/berendsen 300 300 100
run               30 post no
Per MPI rank memory allocation (min/avg/max) = 189.9 | 189.9 | 189.9 Mbytes
Step Temp E_pair E_mol TotEng Press
      30     2564.783   -264015.07            0   -236500.24   -69879.432
      60    1537.4325   -255396.22            0   -238902.74   -6638.7613
Loop time of 12.7893 on 1 procs for 30 steps with 3600 atoms

95.4% CPU use with 1 MPI tasks x no OpenMP threads
unfix             4

thermo_style      custom step atoms c_thermo_temp c_thermo_press ke pe etotal lx ly lz epair

thermo_modify     lost warn

thermo            10


dump xyz          all xyz 100 dumpa*
dump_modify       xyz element Zn O Ag

timestep          0.01
run               10
Per MPI rank memory allocation (min/avg/max) = 190.1 | 190.1 | 190.1 Mbytes
Step Atoms c_thermo_temp c_thermo_press KinEng PotEng TotEng Lx Ly Lz E_pair
      60     3600    1537.4325   -6639.0242    16493.476   -255396.22   -238902.74       48.739      48.7391      52.0544   -255396.22
      70     3600    1549.2299   -6650.0208    16620.038   -255522.82   -238902.79       48.739      48.7391      52.0544   -255522.82
Loop time of 4.41527 on 1 procs for 10 steps with 3600 atoms

Performance: 0.002 ns/day, 12264.632 hours/ns, 2.265 timesteps/s
95.2% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.6649     | 3.6649     | 3.6649     |   0.0 | 83.01
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00031424 | 0.00031424 | 0.00031424 |   0.0 |  0.01
Output  | 5.4598e-05 | 5.4598e-05 | 5.4598e-05 |   0.0 |  0.00
Modify  | 0.74991    | 0.74991    | 0.74991    |   0.0 | 16.98
Other   |            | 9.227e-05  |            |       |  0.00

Nlocal:    3600 ave 3600 max 3600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    4072 ave 4072 max 4072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    869216 ave 869216 max 869216 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 869216
Ave neighs/atom = 241.449
Neighbor list builds = 0
Dangerous builds = 0


region            slab2 block 0 48 45 48 0 50
create_atoms   3 random 1 99078 slab2
Created 1 atoms
group             slab region slab2
1 atoms in group slab
set               group slab type 3
  1 settings made for type
velocity          slab set 0.0 -0.4 0.0 units box

run               5000
Per MPI rank memory allocation (min/avg/max) = 190.2 | 190.2 | 190.2 Mbytes
Step Atoms c_thermo_temp c_thermo_press KinEng PotEng TotEng Lx Ly Lz E_pair
      70     3601    3470.8064    981.72727    37244.933   -255525.96   -218281.02       48.739      48.7391      52.0544   -255525.96
      80     3601    3482.6657    971.79813    37372.194   -255653.27   -218281.07       48.739      48.7391      52.0544   -255653.27
      90     3601    3494.5852    958.84907    37500.101   -255781.23   -218281.13       48.739      48.7391      52.0544   -255781.23
     100     3601    3506.5603     945.9426    37628.605   -255909.78   -218281.18       48.739      48.7391      52.0544   -255909.78
     200     3601    3628.3679    690.59843    38935.711   -257217.35   -218281.64       48.739      48.7391      52.0544   -257217.35
     300     3601    3750.8578    275.92884    40250.141   -258532.19   -218282.05       48.739      48.7391      52.0544   -258532.19
     400     3601    3869.9678   -261.87766      41528.3   -259810.74   -218282.44       48.739      48.7391      52.0544   -259810.74
     500     3601    3982.2294   -890.70069     42732.97   -261015.89   -218282.92       48.739      48.7391      52.0544   -261015.89
     600     3601    4084.8547   -1578.8049    43834.233   -262117.67   -218283.44       48.739      48.7391      52.0544   -262117.67
     700     3601    4175.7613   -2297.1076    44809.744   -263093.75      -218284       48.739      48.7391      52.0544   -263093.75
    ... ...
    ... ...
    ... ...
    4000     3601    4581.0565   -2390.1814    49158.934   -267455.27   -218296.33       48.739      48.7391      52.0544   -267455.27
    4010     3601    4582.8512   -2340.2268    49178.192    -267474.5   -218296.31       48.739      48.7391      52.0544    -267474.5
    4020     3601    4584.5863   -2289.4176    49196.811   -267493.13   -218296.32       48.739      48.7391      52.0544   -267493.13
    4030     3601    4586.2618    -2239.991    49214.791   -267511.15   -218296.36       48.739      48.7391      52.0544   -267511.15
    4040     3601    4587.8777   -2186.9993    49232.131   -267528.52   -218296.39       48.739      48.7391      52.0544   -267528.52
    4050     3601    4589.4338   -2135.9998    49248.829   -267545.23    -218296.4       48.739      48.7391      52.0544   -267545.23
    4060     3601    4590.9294   -2077.9049    49264.878   -267561.28    -218296.4       48.739      48.7391      52.0544   -267561.28
    4070     3601    4592.3643   -2018.7416    49280.277   -267576.63   -218296.36       48.739      48.7391      52.0544   -267576.63
    4080     3601     4593.739   -1964.2961    49295.029   -267591.34   -218296.31       48.739      48.7391      52.0544   -267591.34
    4090     3601    4595.0532    -1908.473    49309.131   -267605.46   -218296.32       48.739      48.7391      52.0544   -267605.46
    4100     3601     4596.307   -1849.0406    49322.585   -267618.91   -218296.32       48.739      48.7391      52.0544   -267618.91
    4110     3601    4597.5005   -1791.8264    49335.392   -267631.73   -218296.34       48.739      48.7391      52.0544   -267631.73
    4120     3601    4598.6331    -1733.002    49347.546   -267643.89   -218296.34       48.739      48.7391      52.0544   -267643.89
    4130     3601    4599.7054   -1671.0005    49359.054   -267655.43   -218296.38       48.739      48.7391      52.0544   -267655.43
    4140     3601    4600.7169   -1608.4384    49369.908   -267666.32   -218296.41       48.739      48.7391      52.0544   -267666.32
    4150     3601    4601.6674   -1548.2892    49380.107   -267676.48   -218296.37       48.739      48.7391      52.0544   -267676.48
    4160     3601    4602.5583   -1481.4476    49389.667   -267686.04   -218296.37       48.739      48.7391      52.0544   -267686.04
    4170     3601      4603.39   -1416.5297    49398.592      -267695   -218296.41       48.739      48.7391      52.0544      -267695
    4180     3601    4604.1625   -1351.5291    49406.882   -267703.31   -218296.43       48.739      48.7391      52.0544   -267703.31
    4190     3601    4604.8761   -1285.4809     49414.54   -267710.99   -218296.45       48.739      48.7391      52.0544   -267710.99
    4200     3601    4605.5319   -1218.1313    49421.577   -267718.08   -218296.51       48.739      48.7391      52.0544   -267718.08
    4210     3601    4606.1289   -1152.5652    49427.984   -267724.47   -218296.48       48.739      48.7391      52.0544   -267724.47
    4220     3601    4606.6678   -1084.3342    49433.766   -267730.26   -218296.49       48.739      48.7391      52.0544   -267730.26
    4230     3601    4607.1503   -1014.7277    49438.943   -267735.39   -218296.45       48.739      48.7391      52.0544   -267735.39
    4240     3601    4607.5773   -948.09035    49443.525   -267739.96   -218296.44       48.739      48.7391      52.0544   -267739.96
    4250     3601
 
Segmentation fault (core dumped)

---------------------------------------------------------------------------------------------------------------------------------------------------------------
I also used fix deposit "fix 6 add2 deposit 20 3 20 912346 region slab2 near 1.0 vy -0.01 -0.01", but this problem also appears.
I cannot sovle it and I hope to get some advices from you. Thank you very much!


Best regards!
Yang