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Re: [lammps-users] compute temp without removing the bias

# Re: [lammps-users] compute temp without removing the bias

 From: Mostafa Nejatolahi Date: Mon, 10 Jul 2017 22:59:15 +0430

### thanks a lot!

Mostafa Nejatolahi
Ph.D. student at Department of Mechanical Engineering
Shiraz University

On Mon, Jul 10, 2017 at 10:37 PM, Axel Kohlmeyer wrote:

On Mon, Jul 10, 2017 at 1:52 PM, Mostafa Nejatolahi wrote:

Thanks for the reply.

Unfortunately, I am still confused.

1-    The source code file of compue temp/region (the attached file) contains several parts about removing the bias velocity. Therefore, at least there should be a way for this compute to remove the bias. As I could not find any option for that, I concluded that this fix always removes the bias!

​please don't make claims about code, when you don't understand it. the whole point about temperature biases applies to using a thermostat, but *not* to computing a temperature. compute temp/region can be use to compute the temperature of the region (see the compute_scalar() function), but it can *also* be used as a temperature bias for a thermostat algorithm, i.e. to only thermostat atoms in that region. those "bias" functions will not be called, if you use the compute simply to compute the temperature.​

2-    Also in sec 6.16 it is written that this compute calculates the velocity biases directly and removes it when computing the thermal temperature:

These compute commands calculate temperature, and the compute pressure command calculates pressure.

All but the first 3 calculate velocity biases directly (e.g. advection velocities) that are removed when computing the thermal temperature.

rather than arguing with documentation fragments that confuse you, ​why don't you just make ​test?
set up a system, where the region covers the entire system, and compare the output of compute temp with compute temp/region and compute temp/com, which is the one compute that *does* remove the COM velocity before computing the temperature.

axel.

Regards

On Mon, Jul 10, 2017 at 9:36 PM, Axel Kohlmeyer wrote:

On Mon, Jul 10, 2017 at 12:36 PM, Mostafa Nejatolahi wrote:
Dear Axel,

According to sec. 6.16 of the manual, "compute temp/region" removes the bias velocity. I could not see any option to force this command to calculate the temp without removing the bias.

​i think you are misreading this section.
there is no indication in the documentation for compute temp/region (or in the source code), that there is a center of mass velocity bias removed.

​axel.​

Regards.

Mostafa Nejatolahi
Ph.D. student at Department of Mechanical Engineering
Shiraz University

On Mon, Jul 10, 2017 at 3:40 PM, Axel Kohlmeyer wrote:

On Sat, Jul 8, 2017 at 5:47 PM, Mostafa Nejatolahi wrote:
Dear all,

I am considering if someone knows how I could compute the temperature of a group or a region without removing the bias (velocity of com) from the velocities. Since I wanna use the computed temperature in a fix_modify command, it is necessary to use a "temp" calculating "compute" like compute temp or compute temp/region.

​so why don't you use compute temp/region?

axel.​

Regards

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.