[DFTB-Plus-User] XLBOMD

[Ben Hourahine]

Hello Gu,

Depending on what data you need to gather, you could instead try running
an ensemble of simulations  (i.e. separate calculations with different
random seeds) and then calculate property averages afterwards or select
more stable structures if annealing.

For time independent properties this is equivalent to a single long
calculation, but can be parallelized much better. Unfortunately it
doesn't help for things like vibrational mode calculations or other time
ordered properties.

There is some literature discussion that this ensemble method (when
applicable) is more efficient at sampling phase space than a single long
calculation (alternatively you could also use accelerated method like
plumed or similar, again if relevant).

Regards

Ben

On 12/06/2020 02:41, 10174602105 wrote:
> Thank you so much!
>
> ---Original---
> *From:* "Sharma SRK Chaitanya Yamijala"<sharmajncasr at gmail.com>
> *Date:* Thu, Jun 11, 2020 03:42 AM
> *To:* "User list for DFTB+ related
> questions"<dftb-plus-user at mailman.zfn.uni-bremen.de>;
> *Cc:* "tz878"<tz878 at nyu.edu>;
> *Subject:* Re: [DFTB-Plus-User] XLBOMD
>
> You can run an NVT calculation (without XLBOMD) for a few picoseconds
> and then use the final positions and velocities for your XLBOMD NVE
> simulation. Since you ran an NVT first, the velocities of the atoms
> will be at your target temperature.
>
> I hope this procedure will probably help you to start an XLBOMD-NVE
> simulation at the required temperature.
>
> --------------------------------------------------------------------
> SRK *Chaitanya* Sharma, Yamijala.
> https://scholar.google.com/citations?hl=en&user=IglNkREAAAAJ
> <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fhl%3Den%26user%3DIglNkREAAAAJ&data=02%7C01%7Cbenjamin.hourahine%40strath.ac.uk%7Cffdfb6d3bdc247b31b1f08d80e71cd3f%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637275229512140106&sdata=3cpGTJz5AvAcmWxWCHWrrrBErqsIQ3wVwlu29YUhHEg%3D&reserved=0>
>
>
>
> On Wed, Jun 10, 2020 at 9:30 AM 10174602105
> <10174602105 at stu.ecnu.edu.cn <mailto:10174602105 at stu.ecnu.edu.cn>> wrote:
>
>     Hi DFTB+ community,
>     I am a new user of DFTB+ code. I am trying to speed up SCC MD, so
>     I use the fast XL-BOMD method. However, it does not work.
>     Here is the Diver block:
>     Driver = VelocityVerlet {
>       TimeStep [fs] = 0.5
>       # Use thermostat to maintain temperature
>       Thermostat = NoseHoover {
>         Temperature [Kelvin] = 2000
>         CouplingStrength [cm^-1] = 3200
>       }
>       # extended Lagrangian dynamics, using the 'fast' option
>       XlbomdFast {
>         IntegrationSteps = 5
>         Scale = 0.5 
>         TransientSteps = 10
>       }
>       Steps = 40
>       MovedAtoms = 1:-1
>     }
>      
>     I got the following error:
>     ERROR!
>     -> XLBOMD does not work with thermostats yet
>     Done.
>      
>     Must it be NVE? Then how can I control the temperature with
>     XLBOMD? Can someone please offer some advice?
>     PS: The system is about C, H, O, N atoms.
>      
>     Thank you,
>     Shuangfei Gu
>     _______________________________________________
>     DFTB-Plus-User mailing list
>     DFTB-Plus-User at mailman.zfn.uni-bremen.de
>     <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
>     https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>     <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.zfn.uni-bremen.de%2Fcgi-bin%2Fmailman%2Flistinfo%2Fdftb-plus-user&data=02%7C01%7Cbenjamin.hourahine%40strath.ac.uk%7Cffdfb6d3bdc247b31b1f08d80e71cd3f%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637275229512140106&sdata=NiYnwKo1hYWax2fYcwPbsjgn9qZJT%2FFRREbUMHQP8Ag%3D&reserved=0>
>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.zfn.uni-bremen.de%2Fcgi-bin%2Fmailman%2Flistinfo%2Fdftb-plus-user&data=02%7C01%7Cbenjamin.hourahine%40strath.ac.uk%7Cffdfb6d3bdc247b31b1f08d80e71cd3f%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637275229512160100&sdata=MP685ZB2Q6i3ot1NjZ9SAfZ%2FiYkqH%2FOxvPzmT1%2BYGeE%3D&reserved=0

-- 
        Dr.  B.  Hourahine,  Senior  lecturer
            SUPA, Department  of  Physics,
             University  of  Strathclyde,
              John  Anderson  Building,
          107 Rottenrow, Glasgow G4 0NG, UK.                    
  +44 141 548 2325, benjamin.hourahine at strath.ac.uk

The  Department is  a partner  in SUPA,  the Scottish
            Universities Physics Alliance

The University  of Strathclyde  is a  charitable body,
       registered in Scotland, number SC015263

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20200612/5d54bf1d/attachment-0001.htm>