错误汇总

一、ERROR on proc 0: Neighbor list overflow, boost neigh_modify one or page

出现这个错误的直接原因是体系中某些原子的近邻数超过了2000个（除非你使用neigh_modify命令增加了允许的近邻数），而导致这个错误的可能因素有：
1.初始结构有问题，比如原子分布过于密集。这种情况在一开始就会出错。
2.截断半径设置的太大了，比如大于10A。可以通过命令neighbor，减小截断半径来解决。
3.势参数设置有问题，这种情况一般是在运行一些步后才会出错。

下面是英文原文：

the reason is that you have more than 2000 neighbors for a single atom (unless you used neigh_modify), which most commonly happens with the following scenarios:
- your initial structure is bad (too dense). in this case the error would happen right at the beginning
- your cutoff it very large (say, 8x-10x sigma)
- your potential parameters are bad. in this case the error would happen after running some MD steps.

 

二、create_atoms

 region aa block -30 110 -30 110 -30 70

read_data data.681.218_msGnH1 extra/atom/types 2 extra/bond/types 1 extra/angle/types 1

molecule spce spce.mol offset 5 6 12 13 1

lattice sc 4

create_atoms 0 region aa mol spce 123 units box

#change_box all x final -20 80 y final -50 110 z final -50 50 units box

change_box all x final -30 110 y final -30 110 z final -30 70 units box

 注意：如果只是改region和change_box，会报错，必须先修改read_data中xyz范围，才可。故read_data中xyz范围在create_atom中至关重要。

 

三、固定原子并求质心

固定：fix spring/self

　eg: fix 1 G1 spring/self 10.0 xyz

质心：compute com

eg: compute com1 G1 com

　　thermo_style custom c_com1[1] c_com1[2] c_com1[3]

　　thermo 200