Dear All,
I am using LAMMPS (14 Feb 2014) and have some questions :
1.I am using read_restart command and get the error: Atom sorting has bin size = 0.0 (…/atom.cpp:1578).Manual tells me that :
Atom sorting has bin size = 0.0
The neighbor cutoff is being used as the bin size, but it is zero. Thus you must explicitly list a bin size
in the atom_modify sort command or turn off sorting.
However,I am still confused that I have never used such a command like ‘atom_modify sort’ before in my input script.Why I must explicitly list a bin size in the atom_modify sort command or turn off sorting when using read_restart command?
2.Then,I use 'atom_modify sort 1000 0.0 'command which is the default setting according to manual and still get the same error.I wonder how to deal with the problem and get the same result like the input script not using read_restart command.
3.lammps can compute rdf. However,the expressions of different papers may have some differences when computing rdf.Therefore,I wonder the expressions given by lammps,and have it compared to those from other papers.
Dear All,
I am using LAMMPS (14 Feb 2014) and have some questions :
1.I am using read_restart command and get the error: Atom sorting has bin
size = 0.0 (../atom.cpp:1578).Manual tells me that :
Atom sorting has bin size = 0.0
The neighbor cutoff is being used as the bin size, but it is zero. Thus you
must explicitly list a bin size
in the atom_modify sort command or turn off sorting.
However,I am still confused that I have never used such a command like
'atom_modify sort' before in my input script.Why I must explicitly list a
bin size in the atom_modify sort command or turn off sorting when using
read_restart command?
this sounds like you triggered a bug. have you tried the current
version of LAMMPS?
2.Then,I use 'atom_modify sort 1000 0.0 'command which is the default
setting according to manual and still get the same error.I wonder how to
deal with the problem and get the same result like the input script not
using read_restart command.
see my previous answer. if you still have problems, please provide a
minimal(!) input example that reproduces it and post it to the list.
3.lammps can compute rdf. However,the expressions of different papers may
have some differences when computing rdf.Therefore,I wonder the expressions
given by lammps,and have it compared to those from other papers.
the (spherical) radial distribution function is a well defined entity.
you can find it in any statistical mechanics text book that is worth
its money.
I am using the current version of LAMMPS.My input script is as follow:
read_restart restart.nve
timestep 0.001
fix 1 all nve
reset_timestep 0
velocity all set 14 0.0 0.0 units box sum yes
dump 2 all cfg 20 dump._*.cfg mass type xs ys zs id type fx fy fz
dump_modify 2 element Al
dump_modify 2 sort id
thermo 1000
thermo_style custom step temp etotal enthalpy ke pe press
run 10000
I am using the current version of LAMMPS.My input script is as follow:
This is useless. You also need to provide a script to generate the restart.
Also, I asked for a minimal script, I.e. Something that has the minimum amount of script commands and the minimum number of atoms to reproduce the issue.
The error is likely b/c you haven’t defined a pair style
in your script, and hence no cutoff in your system.
So you have to turn off atom sorting (which is on by default)
since it expects some length scale (the cutoff) to be defined.
Do this with atom_modify sort 0 0. You just reset atom_modify
sort to the default values, which left it on.