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标题: 请教如何用LAMMPS生成双谱（bispectrum）描述符 [打印本页]

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Author: TwilyAbyss 时间: 2025-9-28 00:12
标题: 请教如何用LAMMPS生成双谱（bispectrum）描述符
本帖最后由 TwilyAbyss 于 2025-9-28 00:16 编辑

各位老师好！想请教您一个关于LAMMPS的问题。我正在用LAMMPS生成“双谱”（bispectrum）分量，LAMMPS手册上的命令是compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...，我输入文件如下：
# LAMMPS input script for bispectrum descriptor calculation
# Based on LAMMPS documentation: https://docs.lammps.org/

# Initialize simulation
units          real
boundary       p p p
atom_style    atomic

# Read structure from .lmp file
read_data    2_DABLEY.Co_ligand3_2_PETSUC.Co_ligand2.lmp

# Set masses for atom types (adjust based on your actual atom types)
mass          1       58.933000    # Co
mass          2       12.011000    # C
mass          3       1.008000    # H
mass          4       30.974000    # P
mass          5       15.999000    # O

# Set neighbor list parameters
neighbor       20.0 bin
neigh_modify delay 0 every 1 check yes one 50000 page 500000

# Define zero potential (minimal requirement for SNAP calculations)
pair_style    zero 100.0
pair_coeff    * *

# Basic bispectrum descriptor calculation
compute       bispectrum all sna/atom 1.4 0.95 8 3.0 3.0 1.8 3.0 3.0 1.0 1.0 1.0 1.0 1.0 rmin0 0.0
# Set timestep
timestep       0.001

# Output basic bispectrum descriptors
dump          1 all custom 1 bispectrum_basic.dump &
            id type x y z c_bispectrum
dump_modify    1 format float %15.8g

# Run calculation
run          0

# Print completion message
print          "SNAP bispectrum calculation completed."

# Clean up
undump       1
但是运行后会出现报错提示：ERROR on proc 0: Neighbor list overflow, boost neigh_modify one
For more information see https://docs.lammps.org/err0036 (src/npair_bin.cpp:248)想请教一下这个怎么解决呢？我以前没用过LAMMPS，感觉这是一款主打分子动力学的软件，因此不清楚对于生成分子描述符需要的最精简的代码是什么样子的，哪些关键词是冗余的可以去掉？请各位老师指导！

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