[DFTB-Plus-User] XLBOMD

Sat Jun 13 07:20:31 CEST 2020

Thanks a lot!

---Original---
From: "Ben Hourahine"<benjamin.hourahine at strath.ac.uk>
Date: Fri, Jun 12, 2020 19:25 PM
To: "dftb-plus-user"<dftb-plus-user at mailman.zfn.uni-bremen.de>;
Subject: Re: [DFTB-Plus-User] XLBOMD

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

                    On Wed, Jun 10, 2020 at 9:30             AM 10174602105 <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
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