[DFTB-Plus-User] xyz position file not updated with MD run

[Ben Hourahine]

Hello Muhammad,

did the system superheat in the crystalline phase instead of melting, or
not warm up when being thermostated?

When I tested your input, I got a 64 atom Si cell to melt by: 1)
removing an atom to make a nucleation centre and 2) increasing the
temperature in the final phase (~3500 K seemed to be sufficient). The
thermostat settings then looked like:

    Thermostat = NoseHoover {
        Temperature [Kelvin] = TemperatureProfile {
            constant    1    0.0
            linear   1500 3500.0
            constant 2000 3500.0
        }
        CouplingStrength[cm^-1] = 600
        AdaptFillingTemp = Yes
    }

A few things that might be worth adjusting in the input are below:

CouplingStrength[cm^-1] = 600

# This should be similar to the Debye frequency, but seems robust


MaxAngularMomentum = {

    Si = "p"

    # probably the intended choice for that parameter set, but check.
Oddly, using

    # the PBC parameters instead give a noticeably faster run time for me.

}


SCC = No

# probably can avoid the SCC cost in this case as charge transfer is small


Also, the gamma point sampling might be a little small (it depends on
your geometry).

Regards

Ben

On 07/05/17 12:56, Faruq, Muhammad via DFTB-Plus-User wrote:
> Dear Sir
>
> I have run MD simulation with Si atom (512). The problem is that the final position is not updated with the temperature. The xyz file position should be updated when the simulation run for the liquid state. I required xyz file to calculate the RDF. I have checked their is no difference between room temperature and liquid temperature. Could you please help me to solve the problem.
>
> Here is the hsd file-
>
> [maf2mpo at quantum MD_Si_liquid]$ more  MD_in.hsd
> Geometry = GenFormat {
>   <<< Si.gen
> }
> Driver = VelocityVerlet {
>   MovedAtoms =  "1:-1"
> # Steps = 250
>   TimeStep [Femtosecond]= 1.0                #Time interval between two MD steps
>   KeepStationary = No               #Remove translational motion from the system
>   MDRestartFrequency=10
>   Velocities = {}
>   ConvergentForcesOnly = No
>
>   Barostat = {
>     Pressure = 0
>     Timescale [ps] =1
>   }
>
>   Thermostat = NoseHoover {
>     Temperature [Kelvin] = TemperatureProfile { # Temperatures in K
>       constant 1    0.0 # Setting T=10 K for the 0th MD-step
>       linear   250 300.0 # Linearly rising T in  250 steps up to T=300 K
>       linear   1416 2000.0 # Linearly rising T in  1415 steps up to T=2000 K by rate 1.2K/fs
>       constant 2000 2000.0 # Constant T through 2000 steps
> #     exponential 1416 300.0 # Exponential decreasing in 1415 steps to T=300K
>
>     }
>     CouplingStrength[cm^-1]=100
>     IntegratorSteps = 1
>   }
>   OutputPrefix = "final_geo"
> }
>
> Hamiltonian = DFTB {
>   SCC = Yes
>   SCCTolerance = 1.0e-5
>   EwaldParameter = 0.1
>   MaxSCCIterations = 10000
> # AdaptFillingTemp = Yes
>   Mixer = Broyden {
>     MixingParameter = 0.2
>   }
>   MaxAngularMomentum = {
>     Si = "d"
>   }
>    Filling = Fermi {
>     Temperature [Kelvin] = 300
>   }
>
>   SlaterKosterFiles = Type2FileNames {
>     Prefix = "/home/maf2mpo/FAST_cal_Others/DFTB+/sk/matsci-0-3/"
>     Separator = "-"
>     Suffix = ".skf"
>   }
>   KPointsAndWeights = {
>     0.0 0.0 0.0 1.0
>   }
>   ReadInitialCharges = Yes
> }
> Options = {
>   WriteEigenvectors = No
>   WriteResultsTag = Yes
>   WriteDetailedOut = Yes
>   WriteBandOut = Yes
> }
>
>
> Thanks
> Muhammad Faruq
> PhD Researcher, IREET
> I-zone, Room-G10
> University of Bolton
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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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