|From:||Mostafa Nejatolahi <mostafa.nejatolahi@...24...>|
|Date:||Mon, 10 Jul 2017 22:59:15 +0430|
On Mon, Jul 10, 2017 at 1:52 PM, Mostafa Nejatolahi <mostafa.nejatolahi@...24...> 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:
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.
On Mon, Jul 10, 2017 at 9:36 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:On Mon, Jul 10, 2017 at 12:36 PM, Mostafa Nejatolahi <mostafa.nejatolahi@...24...> 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 NejatolahiPh.D. student at Department of Mechanical EngineeringShiraz UniversityOn Mon, Jul 10, 2017 at 3:40 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:On Sat, Jul 8, 2017 at 5:47 PM, Mostafa Nejatolahi <mostafa.nejatolahi@...24...> 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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