计算化学公社

标题: LAMMPS模拟neighbor=0问题求助 [打印本页]

作者
Author: leeru 时间: 2021-11-9 22:04
标题: LAMMPS模拟neighbor=0问题求助
各位专家，我在用MYP势函数模拟CH3NH3PbI3钙钛矿材料时，发现lammps的输出log文件中显示Total # of neighbor = 0，这应该是有问题，但自己又检查不出来，希望各位帮忙指点以下，下面的文本分别是1 输入文件、2 data文件(前部数据)和3 log文件(neighbor部分)。

1，输入文件

# simulation of the MAPbI3 by MYP

# initiate the simulation
clear
units                real
boundary             p p p
dimension          3
atom_style          full
pair_style          hybrid buck/coul/long 10.0 lj/cut/coul/long 10.0
neighbor             2 bin
neigh_modify       every 1 delay 0 check yes

# creat atoms
read_data          "data.MAPbI3"

# set the charge
set                type 1 charge 0.7710 # C
set                type 2 charge -1.1000 # N
set                type 3 charge 0.0230 # Hc
set                type 4 charge 0.5400 # Hn
set                type 5 charge 2.0300 # Pb
set                type 6 charge -1.1300 # I

# set the buckingham potentials
pair_coeff          5 5 buck/coul/long 70359906.6 0.131258 0.0 # Pb-Pb
pair_coeff          5 6 buck/coul/long 103496.1 0.321737 0.0 # Pb-I
pair_coeff          6 6 buck/coul/long 22793.3 0.482217 696.900 # I-I
pair_coeff          1 5 buck/coul/long 32690390.9 0.150947 0.0 # Pb-C
pair_coeff          2 5 buck/coul/long 32690390.9 0.150947 0.0 # Pb-N
pair_coeff          1 6 buck/coul/long 112936.7 0.342426 0.0 # I-C
pair_coeff          2 6 buck/coul/long 112936.7 0.342426 0.0 # I-N

# set the LJ potentials
pair_coeff          1 1 lj/cut/coul/long 0.1094 3.39970 # C-C
pair_coeff          2 2 lj/cut/coul/long 0.1700 3.25000 # N-N
pair_coeff          3 3 lj/cut/coul/long 0.0157 1.96000 # Hc-Hc
pair_coeff          4 4 lj/cut/coul/long 0.0157 1.06910 # H-H
pair_coeff          3 5 lj/cut/coul/long 0.0140 2.70999 # Pb-Hc
pair_coeff          4 5 lj/cut/coul/long 0.0140 2.26454 # Pb-Hn
pair_coeff          3 6 lj/cut/coul/long 0.0574 3.10000 # I-Hc
pair_coeff          4 6 lj/cut/coul/long 0.0574 2.75000 # I-Hn
pair_coeff          1 2 lj/cut/coul/long 0.1346 3.32480 # C-N
pair_coeff          1 3 lj/cut/coul/long 0.0414 2.67980 # C-Hc
pair_coeff          1 4 lj/cut/coul/long 0.0414 2.23440 # C-Hn
pair_coeff          2 3 lj/cut/coul/long 0.0517 2.60500 # N-Hc
pair_coeff          2 4 lj/cut/coul/long 0.0517 2.15950 # N-Hn
pair_coeff          3 4 lj/cut/coul/long 0.0157 1.51450 # Hc-Hn

# group the system
group                MA type 1 2 3 4
group                PbI3 type 5 6

# minimize the system
kspace_style       pppm 0.0001
min_style          cg
minimize             1.0e-4 1.0e-6 1000 10000

# run the simulation
timestep             0.1
thermo             1000
dump                d1 all atom 1000 dump.atom.nvt
dump                d2 all xyz 1000 dump.xyz
fix                1 all nvt temp 5 5 10
run                10000

# write data
write_data          data.restart.MAPbI3
print                "simulation completed"

2 data文件前面
# LAMMPS data file written by OVITO Basic 3.5.4
2592 atoms
6 atom types
0.0 37.7407207488 xlo xhi
0.0 37.643340108 ylo yhi
0.0 37.7814902496 zlo zhi
4.66164e-04 -0.238005426 -9.227586e-04 xy xz yz

Masses

1 12.0107  # C
2 14.0067  # N
3 1.00794  # Hc
4 1.00794  # Hn
5 207.2  # Pb
6 126.90447  # I

Atoms  # full

1 1 1 0.0 5.6391501217 6.2735045668 6.2738370369
2 1 1 0.0 5.5994825507 6.2733507737 12.5707520785
3 1 1 0.0 5.5598149797 6.2731969806 18.8676671201

3. 计算log文件（部分）
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Ave special neighs/atom = 0.0000000
Neighbor list builds = 2
Dangerous builds = 0

作者
Author: 耀眼太阳眼泪 时间: 2022-2-17 21:55
怀疑是你的data文件有问题，

作者
Author: leeru 时间: 2025-7-27 21:58
这个其实没有问题，你去看log文件，里有类似的信息，最后出现neigbhor=0主要原因是hybrid这个造成的，详细参考https://matsci.org/t/mpi-and-neighbor-lists/45137
  Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 6 6 15
  4 neighbor lists, perpetual/occasional/extra = 4 0 0

欢迎光临计算化学公社 (http://bbs.keinsci.com/)