[DFTB-Plus-User] NPT simulation

Goldman, Nir goldman14 at llnl.gov
Tue Oct 12 20:56:17 CEST 2010


Hi Ben et al.,

Along similar lines, I've noticed that the virial stress tensor is always
negative in the XX, YY and ZZ directions when it is added to the total
stress tensor in the main driver.  As a result, in my tests the total
pressure printed in md.out (with the virial stress tensor) is always lower
than that printed to stdout (without the virial stress tensor). Offhand this
would seem to be a sign error in the subroutine getVirialStress, although
admittedly I am still gaining familiarity with the mechanics of the code.

Thanks,

Nir


On 10/11/10 11:27 AM, "Ben Hourahine" <benjamin.hourahine at strath.ac.uk>
wrote:

> 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://BLOCKEDdx.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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