[DFTB-Plus-User] NPT simulation

[Ben Hourahine]

Hello Puja,

The difference is that the pressure in the md.out file includes the
virial pressure term due to the kinetic energy of the atoms, while the
pressure in the standard output does not. This difference needs to be
much clearer in the output, or the contributing terms shown separately.
For your simulation, the values in the md.out file are the correct ones
to use.

The md timestep of 1 fs would be quite long if you were not using a
thermostat, since the O-H bond frequencies are quite high (I use about
0.1 fs, but don't often thermostat). You are also using a quite strong
reselection probability (0.2, so that approximately every 5 MD steps the
velocities will reset). You probably should test the sensitivity of your
results to reducing both of these parameters.

The timescale for the Barostat looks reasonable. As a time, the
parameter is broadly equivalent to the time it would take for the system
pressure to change to the target value in the absence of any
fluctuations. (see Berendsen et al http://dx.doi.org/10.1063/1.448118
for the details, dimensionally its quite a mess though).

Regards

Ben

Puja Goyal wrote:
> Hi all,
> 
> Has anyone tried doing an NPT simulation with DFTB+? I am doing an NPT simulation on a water box and am unable to figure out why
> the pressure printed in the md.out file and in the output are different for a given step? I am using the Andersen thermostat with
> the Berendsen barostat to get an NPT ensemble. The 'driver' section of my input file is as follows:
> 
> Driver = VelocityVerlet {
>   Steps = 50000
>   TimeStep [Femtosecond] = 1.0
>   Thermostat = Andersen {
>     Temperature [Kelvin] = 300.0
>     ReselectProbability = 0.200000000000000
>     ReselectIndividually = No
>     AdaptFillingTemp = Yes
>   }
>   Barostat = {
>     Pressure [Pa] = 101325.0
>     Timescale [ps] = 0.1
>   }
> }
> 
> At step 0, the output is:
> 
>  Pressure:                           0.997522E-04 au     0.293481E+10 Pa
> 
> On the other hand, in the md.out file, I have the following for step 0:
> 
> Pressure:                           0.854304E-04 au     0.251345E+10 Pa
> 
> Could anybody please tell me if my input is OK? Is the timescale value I am using OK (although I am confused by the manual which
> says the timescale is beta/tau which means that if we neglect the unit of beta, the unit should be time^(-1) )?
> 
> I would really appreciate any help.
> 
> Puja.
> 
> 
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-- 
     Dr. B. Hourahine, 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
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registered in Scotland, with registration number SC015263