Dear Lammps-users,

Hi,

I have a question about computing temperature in lammps.

I need to calculate temperature of rigid water in a region of the simulation box.

Therefore I need to define temp in the way that exclude some degree of freedom.It seems to me that after this definition temp/region command still uses the default temp definition.

Because with and without my temp definition thermo_style prints out the same temperature.

Does anyone have any suggestion ?

The related lines of input is as follows:

From the compute temp/region doc page:

Unlike other compute styles that calculate temperature, this compute does not subtract out degrees-of-freedom due to fixes that constrain motion, such as *fix shake* and *fix rigid*. This is because those degrees of freedom (e.g. a constrained bond) could apply to sets of atoms that straddle the region boundary, and hence the concept is somewhat ill-defined. If needed the number of subtracted degrees-of-freedom can be set explicitly using the *extra* option of the *compute_modify* command.

If you can estimate the number of water molecules in the region, you

can use compute_modify extra to subtract the appropriate DOF.

If someone can suggest a better way to do this, I suppose an alternative

could be implemented.

Steve

From the compute temp/region doc page:

Unlike other compute styles that calculate temperature, this compute does

not subtract out degrees-of-freedom due to fixes that constrain motion,

such as *fix shake* <http://lammps.sandia.gov/doc/fix_shake.html> and *fix

rigid* <http://lammps.sandia.gov/doc/fix_rigid.html>. This is because

those degrees of freedom (e.g. a constrained bond) could apply to sets of

atoms that straddle the region boundary, and hence the concept is somewhat

ill-defined. If needed the number of subtracted degrees-of-freedom can be

set explicitly using the *extra* option of the *compute_modify*

<http://lammps.sandia.gov/doc/compute_modify.html> command.If you can estimate the number of water molecules in the region, you

can use compute_modify extra to subtract the appropriate DOF.If someone can suggest a better way to do this, I suppose an alternative

could be implemented.

one way to do this would be to add a "dof" property to each atom

defaulting to 3.0 (or 2 in 2d sims) and then subtract the DOF fraction that

is removed from it (so 0.5 DOF for a bond contstraint, 1/3 for an angle, it

gets a bit messy for (linear) rigid bodies...)

axel.

Hi Steve and AXel,

Thank you for your advice.

I did not understand what Axel mean as I am new in lammps.

I think Steve means the below modification, in hot region for example, that it does not work for me.

Hi Steve and AXel,

Thank you for your advice.

I did not understand what Axel mean as I am new in lammps.

I think Steve means the below modification, in hot region for example,

that it does not work for me.

nobody can help you based on such vague terms as "it doesn't work (for

me)" and a minimal fraction of your input.

if you believe that LAMMPS is not doing something the way it is advertised

in the documentation (or the way you think it should be done),

then you have to provide a small demosntration input that illustrates your

claim and then explain what you see and what you think you should see and

why you believe that it should be like this. double check with the

documentation.

axel.

Dear Axel,

Thank you again.

Yes you are right and I did not send you enough data.

Regards