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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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