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.
Regards
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.
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.
Regards.
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.
http://lammps.sandia.gov/doc/compute_temp_region.html
axel.
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!
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.
Regards
compute_temp_region.cpp (7.4 KB)
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* <http://lammps.sandia.gov/doc/compute.html> calculate
temperature, and the *compute pressure*
<http://lammps.sandia.gov/doc/compute_pressure.html> command calculates
pressure.· *compute temp* <http://lammps.sandia.gov/doc/compute_temp.html>
· *compute temp/sphere*
<http://lammps.sandia.gov/doc/compute_temp_sphere.html>· *compute temp/asphere*
<http://lammps.sandia.gov/doc/compute_temp_asphere.html>· *compute temp/com*
<http://lammps.sandia.gov/doc/compute_temp_com.html>· *compute temp/deform*
<http://lammps.sandia.gov/doc/compute_temp_deform.html>· *compute temp/partial*
<http://lammps.sandia.gov/doc/compute_temp_partial.html>· *compute temp/profile*
<http://lammps.sandia.gov/doc/compute_temp_profile.html>· *compute temp/ramp*
<http://lammps.sandia.gov/doc/compute_temp_ramp.html>· *compute temp/region*
<http://lammps.sandia.gov/doc/compute_temp_region.html>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