[DFTB-Plus-User] Extremely slow MD

[Bálint Aradi]

Dear Abdullah,

first of all, please use the most recent version. Download the binary 
directly from the website or install it via conda, to make sure, it is 
not a compilation problem.

Otherwise, is hard to say. What do you mean by slow. Also, do you use 
parallelism? If yes, which one (OpenMP or MPI)? Does your machine has 
enough RAM? (Maybe the process is swapping?)

Best regards,

Bálint

On 20.04.21 17:11, Abdullah Bin Faheem wrote:
> Dear DFTB+ users,
> 
> I am using DFTB+ 19.1 to run MD of a box of water molecules, with 
> graphene and CaF2 layers (882 atoms) and using the 3ob parameters for 
> DFTB3. However, it takes a very long time to finish even one MD step. I 
> have tried to use different Solvers (ELPA, NTPoly, OMM), but it does not 
> make a difference. I am using the MPI version of DFTB+ and have tried 
> out using 6, 12, 15, and 30 mpi processes, but it does not improve the 
> results. Changing the Mixer from Broyden to Anderson gives the same time 
> results.
> 
> The input file is as follows:
> 
> Geometry = GenFormat {
> 882 S
>   Ca F C O H
>      1 1    0.7202443272E-01    0.7032980539E+01    0.4107560989E+01
>      2 1    0.4004118083E+01    0.6999144781E+01    0.4161273297E+01
>      3 1    0.7890550957E+01    0.7070604493E+01    0.4106813778E+01
>      4 1    0.1168937823E+02    0.7005426600E+01    0.4039285473E+01
>      5 1    0.9944288762E-01    0.2736434439E-01    0.4168457924E+01
> .
> .
> .
>    877 4    0.1421618759E+02    0.6309258063E+01    0.3225699778E+02
>    878 5    0.1353106869E+02    0.6940379596E+01    0.3241309410E+02
>    879 5    0.1509388546E+02    0.6646394136E+01    0.3226620183E+02
>    880 4    0.7717108287E+00    0.7430108512E+01    0.4311866219E+02
>    881 5    0.1500101168E+01    0.6928998668E+01    0.4275502506E+02
>    882 5    0.4968721117E+00    0.7268172745E+01    0.4401107775E+02
> 0.0000 0.0000 0.0000
> 16.500 0.0000 0.0000
> 0.0000 14.900 0.0000
> 0.0000 0.0000 69.000
> }
> Driver = VelocityVerlet {
>    MovedAtoms = 1:-1
>    Steps = 1
>    TimeStep [Femtosecond] = 0.5
>    MDRestartFrequency = 1
>    Thermostat = NoseHoover {
>      Temperature [Kelvin] = 298.00
> CouplingStrength [cm^-1] = 3200
>    }
>    OutputPrefix = "geo_end"
> }
> 
> Hamiltonian = DFTB {
>    Solver = ELPA {
>    Mode = 2
>    }
>    Mixer = Anderson {
>    MixingParameter = 0.2
>    }
>    SCCTolerance = 1.000E-004
>    ForceEvaluation = Dynamics
>    SCC = Yes
>    SlaterKosterFiles = Type2FileNames {
>    Separator = "-"
>    Suffix = ".skf"
>    }
>    Filling = Fermi {
>    Temperature [Kelvin] = 298
>    }
>    MaxSCCIterations = 300
>    ReadInitialCharges = No
>    MaxAngularMomentum {
>      O = "p"
>      H = "s"
>      C = "p"
>      F = "p"
>     Ca = "p"
>    }
>    ThirdOrder = Yes
>    HubbardDerivs {
>     O = -0.1575
>     H = -0.1857
>     C = -0.1492
>     F = -0.1623
>     Ca = -0.0340
>    }
>    Dispersion = DftD3 {
>     Damping = BeckeJohnson {
>      a1 = 0.746
>      a2 = 4.191
>    }
>      s6 = 1.0
>      s8 = 3.209
>   }
>    HCorrection = Damping {
>    Exponent = 4.00
>   }
> KPointsAndWeights = {
>      1 0 0
>      0 1 0
>      0 0 1
>   0.5 0.5 0.5
>    }
> }
> Options {
>    WriteAutotestTag = Yes
>    WriteChargesAsText = Yes
> }
> Parallel {
>    UseOmpThreads = no
>    Groups = 3
>   }
> 
> Is there perhaps something wrong with my approach? Any suggestions would 
> be greatly appreciated. Thank you for your time.
> 
> Regards,
> Abdullah
> 
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> 


-- 
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/


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