Sorry, I foget to upload the logfile.
In my test, this code (or it’s variant) leads to two results:
1.ERROR on proc 0: Too many neighbor bins (src/nbin_standard.cpp:213)
2.particles explosion and it’s temp rises out of control.
These occur in relaxation or direct simulation.
logfile as follow
外部模型读入############## 模具扩孔
read_data D1.data
Reading data file …
orthogonal box = (-69.0555 -100.01835 -69.947249) to (69.18898 100.01367 69.18898)
2 by 3 by 2 MPI processor grid
reading atom labelmap …
reading atoms …
128141 atoms
reading velocities …
128141 velocities
read_data CPU = 0.702 seconds
reset_atom_ids
Resetting atom IDs …
No /omp style for force computation currently active
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
势函数设置 ################### 添加势函数文件---------------------------
#Mg-Y-Zn合金混合势设置
#第一行把所有的势函数类型都列出来
pair_style hybrid meam meam lj/cut 10 lj/cut 5.5 lj/cut 7 lj/cut 7.5 lj/cut 9.5
#Y-Zn-Mg, NULL说明原子类型
pair_coeff * * meam 1 library.meam.txt Mg Y Mg-Y.meam.txt Mg Y NULL NULL
pair_coeff * * meam 2 library.meam.txt Zn Mg Zn-Mg.meam.txt Mg NULL Zn NULL
#设置Y与Zn之间的原子势函数
pair_coeff 2 3 lj/cut 1 0.7271 2.7128
#C-*混合势设置
pair_coeff 4 4 lj/cut 2 6.3695 1.3542 #C-C
pair_coeff 3 4 lj/cut 3 1.1046 1.7157 #Zn-C
pair_coeff 1 4 lj/cut 4 0.7075 1.8445 #Mg-C
pair_coeff 2 4 lj/cut 5 4.1926 2.1411 #Y-C ########### 在混合势中添加C的势函数-------------------------
#pair_modify shift yes
#comm_modify mode single cutoff 10.0 vel yes
组别设置
region wirehead cylinder y 0 0 37 90 100 ###################调整模具空间坐标-------------
group wirehead region wirehead
1872 atoms in group wirehead
group die type 4
64219 atoms in group die
group wire1 type 1
60395 atoms in group wire1
group wire2 type 2
2019 atoms in group wire2
group wire3 type 3
1508 atoms in group wire3
group wire0 union wire1 wire2 wire3
63922 atoms in group wire0
group wire subtract wire0 wirehead
62050 atoms in group wire
能量最小化
min_style cg
minimize 1.0e-8 1.0e-8 100 10000
Hybrid pair style last /omp style lj/cut
Last active /omp style is pair_style lj/cut
Neighbor list info …
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 22 31 22
15 neighbor lists, perpetual/occasional/extra = 15 0 0
(1) pair meam, perpetual, skip from (10)
attributes: full, newton on, omp, cut 9
pair build: skip/omp
stencil: none
bin: none
(2) pair meam, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(3) pair meam, perpetual, skip from (10)
attributes: full, newton on, omp, cut 9
pair build: skip/omp
stencil: none
bin: none
(4) pair meam, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(5) pair lj/cut, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(6) pair lj/cut, perpetual, skip from (12)
attributes: half, newton on, omp, cut 8.5
pair build: skip/omp
stencil: none
bin: none
(7) pair lj/cut, perpetual, skip from (13)
attributes: half, newton on, omp, cut 10
pair build: skip/omp
stencil: none
bin: none
(8) pair lj/cut, perpetual, skip from (14)
attributes: half, newton on, omp, cut 10.5
pair build: skip/omp
stencil: none
bin: none
(9) pair lj/cut, perpetual, skip from (15)
attributes: half, newton on, omp, cut 12.5
pair build: skip/omp
stencil: none
bin: none
(10) neighbor class addition, perpetual
attributes: full, newton on, omp, cut 9
pair build: full/bin/atomonly/omp
stencil: full/bin/3d
bin: standard
(11) neighbor class addition, perpetual
attributes: half, newton on, omp
pair build: half/bin/atomonly/newton/omp
stencil: half/bin/3d
bin: standard
(12) neighbor class addition, perpetual, trim from (13)
attributes: half, newton on, omp, cut 8.5
pair build: trim/omp
stencil: none
bin: none
(13) neighbor class addition, perpetual, trim from (14)
attributes: half, newton on, omp, cut 10
pair build: trim/omp
stencil: none
bin: none
(14) neighbor class addition, perpetual, trim from (11)
attributes: half, newton on, omp, cut 10.5
pair build: trim/omp
stencil: none
bin: none
(15) neighbor class addition, perpetual, trim from (11)
attributes: half, newton on, omp, cut 12.5
pair build: trim/omp
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 49.08 | 55.03 | 66.17 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -81294.555 0 -81294.555 12660.011 3847564.4
100 0 -130054.57 0 -130054.57 12322.07 3847564.4
Loop time of 207.147 on 24 procs for 100 steps with 128141 atoms
99.2% CPU use with 12 MPI tasks x 2 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-81294.5554963493 -130007.004262976 -130054.573550521
Force two-norm initial, final = 3572.7132 210101.83
Force max component initial, final = 931.05661 76701.212
Final line search alpha, max atom move = 4.545859e-09 0.00034867289
Iterations, force evaluations = 100 1065
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
Pair | 183.33 | 195.13 | 202.57 | 43.8 | 94.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 3.8598 | 10.693 | 21.347 | 165.6 | 5.16
Output | 0.000225 | 0.00022625 | 0.000231 | 0.0 | 0.00
Modify | 0.11048 | 0.22873 | 0.43924 | 29.3 | 0.11
Other | | 1.097 | | | 0.53
Nlocal: 10678.4 ave 20663 max 5642 min
Histogram: 8 0 0 0 0 0 0 0 0 4
Nghost: 8282.67 ave 10651 max 6121 min
Histogram: 4 0 0 0 4 0 0 0 0 4
Neighs: 0 ave 0 max 0 min
Histogram: 12 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#write_data DD0M.data
温度,速度,受力初始化及拉拔运动设置
die 刚体rigid wirehead 刚体move wire 计算体nve
velocity wire create 723 77777 dist gaussian mom no rot no
fix 5 wire nve/limit 1.5
fix 31 wire temp/berendsen 723 723 1
fix 10 die rigid single
1 rigid bodies with 64219 atoms
fix 20 wirehead move linear 0 0 0 units box
#fix 30 wire nve
#fix 32 wire langevin 723 723 1 4284
dump 1 all atom 200 DD0E.xyz
thermo 200
thermo_style custom step temp press pe ke vol
thermo_modify lost ignore
run 10000
Hybrid pair style last /omp style lj/cut
Last active /omp style is pair_style lj/cut
Neighbor list info …
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 22 31 22
11 neighbor lists, perpetual/occasional/extra = 11 0 0
(1) pair meam, perpetual, skip from (10)
attributes: full, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on, omp
pair build: halffull/newton/skip/omp
stencil: none
bin: none
(3) pair meam, perpetual, skip from (10)
attributes: full, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(4) pair meam, perpetual, half/full from (3)
attributes: half, newton on, omp
pair build: halffull/newton/skip/omp
stencil: none
bin: none
(5) pair lj/cut, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(6) pair lj/cut, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(7) pair lj/cut, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(8) pair lj/cut, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(9) pair lj/cut, perpetual, skip from (11)
attributes: half, newton on, omp
pair build: skip/omp
stencil: none
bin: none
(10) neighbor class addition, perpetual
attributes: full, newton on, omp
pair build: full/bin/atomonly/omp
stencil: full/bin/3d
bin: standard
(11) neighbor class addition, perpetual, half/full from (10)
attributes: half, newton on, omp
pair build: halffull/newton/omp
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 41.95 | 47.95 | 59.3 Mbytes
Step Temp Press PotEng KinEng Volume
100 701.80415 15170.318 -130210.22 5798.7946 3847566.3
ERROR on proc 0: Too many neighbor bins (src/nbin_standard.cpp:213)
Last command: run 10000