mpirun noticed that the process rank 1 with PID 1981 on node ...

Mahbobe_Abdollahi · January 15, 2017, 10:01am

Dear all,

I want to simulate germanium nanowire with point defect. Defects that I considered are 1% up to 8%. For low percentage, the simulation works fine, But in 8% defect on step 1200000 crashes. Every time that I run simulation, it happens again but on different step such as 1000000 or 1500000! The massage that will be shown is: mpirun noticed that the process rank 1 with PID 1981 on node …
This is a piece of my code.

variable P equal 0.08
variable R equal 20
variable T equal 300
variable L equal 200
variable dt equal 60
variable Thot equal T+{dt}/2.0
variable Tcold equal T-{dt}/2.0

log log.lammpsT$TR$R-P$P
echo both
units metal
atom_style atomic
boundary s s s

######################################## BOX
variable z1 equal 0
variable z2 equal L+20 region box block -100 100 -100 100 {z1} ${z2} units box

create_box 1 box
region nw cylinder z 0 0 $R EDGE EDGE units box
lattice diamond 5.658
create_atoms 1 region nw
######################################## MASS
mass 1 72.64
######################################## VELOCITY
velocity all create $T 87287 mom yes rot yes dist uniform
delete_atoms porosity box P 482793 ######################################## POTENTIAL pair_style tersoff pair_coeff * * SiCGe.tersoff Ge neighbor 2 bin neigh_modify every 50 delay 0 ######################################## REGIONS region fl block INF INF INF INF INF 5 units box group fl region fl region 0 block INF INF INF INF 10 15 units box region hot block INF INF INF INF 15 30 units box group hot region hot region 1 block INF INF INF INF 30 40 units box region 2 block INF INF INF INF 40 50 units box region 3 block INF INF INF INF 50 60 units box region 4 block INF INF INF INF 60 70 units box region 5 block INF INF INF INF 70 80 units box region 6 block INF INF INF INF 80 90 units box region 7 block INF INF INF INF 90 100 units box region 8 block INF INF INF INF 100 110 units box region 9 block INF INF INF INF 110 120 units box region 10 block INF INF INF INF 120 130 units box region 11 block INF INF INF INF 130 140 units box region 12 block INF INF INF INF 140 150 units box region 13 block INF INF INF INF 150 160 units box region 14 block INF INF INF INF 160 170 units box region cold block INF INF INF INF 170 185 units box group cold region cold region 15 block INF INF INF INF 185 190 units box region fr block INF INF INF INF 190 INF units box group fr region fr group 1 region 1 group 2 region 2 group 3 region 3 group 4 region 4 group 5 region 5 group 6 region 6 group 7 region 7 group 8 region 8 group 9 region 9 group 10 region 10 group 11 region 11 group 12 region 12 group 13 region 13 group 14 region 14 group middle subtract all fl fr hot cold ######################################## HOT & COLD fix 1 hot nvt temp {Thot} {Thot} 0.1 fix 2 cold nvt temp {Tcold} ${Tcold} 0.1
fix 5 middle nve
######################################## SETFORCE
fix 3 fl setforce 0 0 0
fix 4 fr setforce 0 0 0
velocity fl set 0 0 0 units box
velocity fr set 0 0 0 units box
########################################
compute hot hot temp
compute 1 1 temp
compute 2 2 temp
compute 3 3 temp
compute 4 4 temp
compute 5 5 temp
compute 6 6 temp
compute 7 7 temp
compute 8 8 temp
compute 9 9 temp
compute 10 10 temp
compute 11 11 temp
compute 12 12 temp
compute 13 13 temp
compute 14 14 temp
compute cold cold temp
########################################
compute ke middle ke/atom
compute pe middle pe/atom
compute stress middle stress/atom NULL virial
########################################
compute J middle heat/flux ke pe stress
variable Jz equal c_J[3]/(3.14*$R*R*140) ######################################## thermo 1000 thermo_style custom step cpu fix ave all ave/time 1 500000 500000 v_Jz c_hot c_1 c_2 c_3 c_4 c_5 c_6 c_7 c_8 c_9 c_10 & c_11 c_12 c_13 c_14 c_cold file ave-r{R}-T$T-dt${dt}-P$P.txt
dump 1 all atom 500000 dump-r${R}-T$T-dt${dt}-P$P.lammpstrj
timestep 0.001
run 2000000

Thanks a lot
Abdollahi

|