Re: [ESPResSo-users] Units

[Peter Košovan]

Hi Robyn,

yes, you are right. The thermostat expects the temperature in units of kT. It does not internally multiply by K.

Regards,

peter

P.S.: please send all questions to the mailing list rather than to individual people. The user guide gives a few reasons why you should do it that way.

2013/7/9 Robyn Latimer (x2011ryq) <address@hidden>

Hi Peter,

Thank you very much for the clarification! My last question is regarding temperature. Is it input as KT into the thermostat?

Robyn
________________________________________
From: Peter Košovan [address@hidden]
Sent: July 9, 2013 10:37 AM
To: Robyn Latimer (x2011ryq); address@hidden
Subject: Re: [ESPResSo-users] Units

Dear Robyn,

Regarding units in Espresso: you can input your quantities in whatever units you like. However, it is your responsibility that your units are consistent, i.e. that you express all quantities with the same physical dimension (length) in the same units - Espresso does not check it for you. It is generally recommended but not necessary to use a system of units where the characteristic sizes and energies of your system are on the order of unity.

Regarding particle size: its definition depends on your potential, i.e. on your model, not on Espresso. Size is a well-defined quantity for hard spheres. If you are using any soft potential, then particle size is partly arbitrary. In the case of LJ potential, the repulsion at distances below r=sigma rises steeply, i.e. the particles rarely appear closer to each other than sigma. The effective "size" of LJ particles increases with increasing sigma, but for a given sigma it also depends on pressure and other interactions. Since the effective size of a particle depends on its interaction potential, you have to come up with your own definition, based on the properties of your potential. You could deduce it e.g. from plotting g(r) of your system.

Regards,

peter

2013/7/9 Robyn Latimer (x2011ryq) <address@hidden<mailto:address@hidden>>

Hello everyone,

I know there have been a few questions about units in Espresso asked already, but after reading them I'm still a little confused. I'm doing a dpd simulation, and the first thing I'm having trouble understanding is how to input the size of particles . There is no input for particle size that I can see, is the default size one? Should I scale all other lengths in the simulation by the size of the particle I want to use? I've read that you can input particle size as sigma for lj potential for example, however I'm not using lj potential but rather a tabulated potential.

I have a few more questions, but this is the main one . Any help would be greatly appreciated!

Thanks a lot,
Robyn



--
Dr. Peter Košovan

Deparmtent of Physical and Macromolecular Chemistry
Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie
Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/<http://www.natur.cuni.cz/chemistry/fyzchem/>
Tel. +420221951290
Fax +420224919752

--

Dr. Peter Košovan

Deparmtent of Physical and Macromolecular Chemistry

Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie

Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951290

Fax +420224919752