Hi there, I am recently want to try running an oxidation process.
Here is my codes and report from the cluster.
it can run the minimize part. After the minimization,it seems that it stop after printing" setting up verlet run".
Can you help me?
Thank you So much!
Lammps version is “stable 29Sep2021”
I removed the command that may not work as a key function.
######### basic setting
package omp 4 neigh no
units metal
boundary p p f
atom_style charge
read_restart restarta1000.equil
timestep 0.0001
set type 14 charge 0
thermo 1
thermo_modify lost ignore
neighbor 2.5 bin
neigh_modify delay 0 check yes
mass 1 12.0107. ### carbon atom
mass 2 12.0107 ### carbon atom
mass 3 12.0107 ### carbon atom
mass 4 15.9990 ### oxygen atom
######## set the pair style
pair_style reaxff/omp NULL
pair_coeff * * ./ffield.reax.CHONSi C C C O
######## basic region area define
fix 0 all wall/reflect zhi EDGE
region inbox block 0 15.132778 0 15.132778 0 89.170750 units box ##### simulation box size
group ino type 4
group exit dynamic ino region inbox every 1000
######## define C atoms that stay at the bottom and can move
region moveall block 0 15.132778 0 15.132778 0.01 30.170750 units box
group allf type 1 2 3
group allfree dynamic allf region moveall every 1000
########## create O atom randomly in the empty space-----create 500 pair O2
variable npart equal 1000
region creatO block 0 15.132778 0 15.132778 32 89.170750 units box
variable a loop 500
label loopa
variable x1 equal random(1.2,14.0,$a+312314)
variable y1 equal random(1.2,14.0,$a+32423423)
variable z1 equal random(34.4,84.1,a+425342)
variable xa equal {x1}
variable ya equal {y1}
variable za equal {z1}
variable alpha1 equal random(0.0,360,$a+314133123)
variable alpha2 equal random(0.0,360,a+234242523)
variable a1 equal {alpha1}
variable a2 equal {alpha2}
variable x2 equal {xa}+1.21cos({a2})*cos({a1})
variable y2 equal {ya}+1.21*cos({a2})sin({a1})
variable z2 equal {za}+1.21sin({a2})
create_atoms 4 single {xa} {ya} {za} units box
create_atoms 4 single {x2} {y2} ${z2} units box
variable xa delete
variable ya delete
variable za delete
variable x1 delete
variable y1 delete
variable z1 delete
variable x2 delete
variable y2 delete
variable alpha1 delete
variable alpha2 delete
variable a1 delete
variable a2 delete
next a
jump SELF loopa
################### fixs command use langevain for O to maintain O kinetic energy and reaxff for reaction
group newo type 4
fix 1 fixd setforce 0.0 0.0 0.0# set those atoms no force #### fixd is the lowest C group id
fix 5 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 2 all nve
fix 3 allfree temp/berendsen 573 573 0.0002 ##### allfree is the substrate of all C atoms group id
delete_atoms overlap 0.5 newo newo
reset_atom_ids
group onlyo dynamic newo region creatO every 10
minimize 1.0e-8 1.0e-8 10000 10000
velocity newo create 90424 77623928 rot yes
fix 6 onlyo langevin 90424 90424 0.005 21345643
fix 7 all balance 1 1.0 shift z 1 1.0
####### compute and output
compute 1 leftc coord/atom cutoff 2.0 1*2
compute 2 leftc property/atom z
compute 3 newo temp
thermo_style custom step atoms c_3 c_Tfilm
thermo_modify lost warn flush yes
thermo 1
####################### end for lammps code
########################### the end of the out put from the hpc
Total # of neighbors = 1452363
Ave neighs/atom = 851.32649
Neighbor list builds = 2
Dangerous builds = 0
WARNING: New thermo_style command, previous thermo_modify settings will be lost (…/output.cpp:689)
Last active /omp style is pair_style reaxff/omp
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 15
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair reaxff/omp, perpetual
attributes: half, newton off, ghost, omp
pair build: half/bin/newtoff/ghost/omp
stencil: full/ghost/bin/3d
bin: standard
(2) compute coord/atom, occasional
attributes: full, newton on, omp
pair build: full/bin/atomonly/omp
stencil: full/bin/3d
bin: standard
(3) fix qeq/reaxff/omp, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Setting up Verlet run …
Unit style : metal
Current step : 3300974
Time step : 0.0001
slurmstepd: error: *** JOB 11527290 ON n0119.savio3 CANCELLED AT 2022-02-21T13:42:31 ***