fix shake error

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1

Dear Lammps users,

I am using fix shake along with fix nve while minimizing my system, corresponding lines are:
fix 1 all nve
fix 2 all shake 0.000001 20 1000 b 1 a 1

resulting an error

ERROR: Shake clusters are connected (fix_shake.cpp:958)

can anyone suggest how to get rig of this error?

Thanks

2

If you look at the errors page (http://lammps.sandia.gov/doc/Section_errors.html), you'll see that your error message means "A single cluster specified by the fix shake command must have a single central atom with up to 3 other atoms bonded to it." So I assume that there are atoms in your simulation which don't follow this topology. What is it you're trying to run?

3

Dear Lammps users,

I am using fix shake along with fix nve while minimizing my system,

huh??
neither "fix nve" nor "fix shake" are active during minimizations.
both only make to be used in an MD. please have a closer
look at the documentation.

corresponding lines are:
fix 1 all nve
fix 2 all shake 0.000001 20 1000 b 1 a 1

resulting an error

ERROR: Shake clusters are connected (fix_shake.cpp:958)

this is a documented limitation of fix shake.
please have a closer look at the documentation.

can anyone suggest how to get rig of this error?

you'll have to implement a "better" version of SHAKE.
it has been explained many, many times on this
mailing list, why the current code has this limitation
and why nobody cares to lift it.

axel.

4

> Dear Lammps users,
>
> I am using fix shake along with fix nve while minimizing my system,

huh??
neither "fix nve" nor "fix shake" are active during minimizations.
both only make to be used in an MD. please have a closer
look at the documentation.

I am trying to minimize system to extremely low thermal state in order to
attain least possible forces on atoms through a repeated cycle of NVE run
(resetting all velocities to zero at the start of run), where I am using
fix nve and fix shake.

5

> Dear Lammps users,
>
> I am using fix shake along with fix nve while minimizing my system,

huh??
neither "fix nve" nor "fix shake" are active during minimizations.
both only make to be used in an MD. please have a closer
look at the documentation.

I am trying to minimize system to extremely low thermal state in order to
attain least possible forces on atoms through a repeated cycle of NVE run
(resetting all velocities to zero at the start of run), where I am using
fix nve and fix shake.

Dear Jackson,
my system is CNT with non-periodic and shrink-wrapped boundary, do you
think changing to periodic boundary will help?