[DFTB-Plus-User] MD problems
R.Perez Garcia
r.perez.garcia at student.rug.nl
Wed Oct 3 01:55:02 CEST 2012
Dear Jianbing Niu,
I am also very new in DFTB, and I work with fullerenes, but from my experience it is better to run smaller number of step each time, and then join th resulting trajectories.
Maybe at the beginning of the simulation if your system has a lot of tensions is better to use a smaller time step for a few iterations to let the CNT to relax.
I hope my answer is not wrong for your case
Best regards: R
On 02-10-12, "Niu, Jianbing" <JianbingNiu at my.unt.edu> wrote:
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> Dear all,
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> I am Jianbing Niu, I am trying to simulate carbon nanotube growth with catalyst via DFTB+MD. But I got errors--Failure in diagonalisation routine dsygvd, non-positive definite overlap--all the time, and the model has been ConjugateGradient relaxed.
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> Below is my input file, and if i change the timestep=0.1 fs and couplingstrenth=1, the code can run but the model did not change much. In literature, the timestep was set to 1 fs, is much larger than mine. Could you check it for me?
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> Thank you very much and regards.
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> Jianbing
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> Geometry = GenFormat {
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> <<< "geom.gen"
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> }
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> Driver = VelocityVerlet {
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> timestep [Femtosecond]= 1
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> steps = 1000000
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> MovedAtoms = 1:-1
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> thermostat = NoseHoover{
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> Temperature[Kelvin] = 1500.05
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> CouplingStrength = 100
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> }
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> OutputPrefix = "geom_out2.out"
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>
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> }
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> Hamiltonian = DFTB {
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> SCC = Yes
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> SCCTolerance = 1e-005
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> MaxSCCIterations = 1000
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> MaxAngularMomentum = {
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> C = "p"
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> Fe = "d"
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> }
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> Eigensolver = DivideAndConquer{}
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> Filling = Fermi {
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> Temperature [Kelvin] = 300.0
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>
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> }
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> SlaterKosterFiles = {
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> C-C = "C-C.skf"
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> C-Fe = "C-Fe.skf"
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> Fe-C = "Fe-C.skf"
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> Fe-Fe = "Fe-Fe.skf"
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> }
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> #ReadInitialCharges = Yes
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> Mixer = Broyden {
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> MixingParameter = 0.2
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> CachedIterations = -1
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> InverseJacobiWeight = 0.01
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> MinimalWeight = 1
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> MaximalWeight = 100000
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> WeightFactor = 0.01
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> }
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> }
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> Options = {
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> #CalculateForces = No
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> WriteEigenvectors = No
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> WriteDetailedXML = No
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> WriteAutotestTag = No
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> WriteResultsTag = Yes
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> WriteDetailedOut = Yes
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> WriteBandOut = No
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> AtomResolvedEnergies = No
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> #RestartFrequency = 20
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> RandomSeed = 0
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> WriteHS = No
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> WriteRealHS = No
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> MinimiseMemoryUsage = No
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> ShowFoldedCoords = No
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> }
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> ParserOptions = {
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> WriteHSDInput = Yes
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> WriteXMLInput = No
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> StopAfterParsing = No
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> ParserVersion = 4
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> IgnoreUnprocessedNodes = No
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> }
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> Analysis = {
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> ProjectStates = {}
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> }
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>
> geom.gen
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> 102 C
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> Fe C
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> 1 1 -1.46E+00 -1.66E+00 7.19E+00
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> 2 1 9.31E-01 -1.97E+00 7.20E+00
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> 3 1 -5.96E-01 4.74E-01 7.01E+00
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> 4 1 1.68E+00 2.83E-01 7.34E+00
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> 5 1 -2.22E+00 -1.44E+00 9.51E+00
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> 6 1 1.49E+00 -2.96E+00 9.31E+00
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> 7 1 -7.08E-01 -3.21E+00 8.72E+00
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> 8 1 -1.08E+00 1.23E+00 9.34E+00
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> 9 1 -2.75E+00 2.21E-01 7.96E+00
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> 10 1 1.46E+00 1.23E+00 9.54E+00
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> 11 1 1.29E-01 -8.40E-01 9.03E+00
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> 12 1 2.63E+00 -9.13E-01 9.14E+00
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> 13 1 4.54E-01 2.38E+00 7.81E+00
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> 14 1 -2.03E+00 -6.67E-01 1.17E+01
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> 15 1 1.80E+00 -1.82E+00 1.13E+01
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> 16 1 -3.96E-01 -2.41E+00 1.10E+01
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> 17 1 -1.44E+00 1.86E+00 1.17E+01
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> 18 1 -3.14E+00 7.46E-01 1.03E+01
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> 19 1 1.12E+00 2.20E+00 1.18E+01
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> 20 1 1.63E-01 6.41E-02 1.13E+01
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> 21 1 2.65E+00 2.90E-01 1.13E+01
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> 22 1 -2.09E-02 3.13E+00 1.01E+01
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> 23 2 3.49E+00 2.55E-01 1.44E+01
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> 24 2 3.28E+00 1.01E+00 1.32E+01
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> 25 2 2.30E+00 2.80E+00 1.45E+01
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> 26 2 2.66E+00 2.26E+00 1.33E+01
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> 27 2 1.03E+00 3.48E+00 1.46E+01
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> 28 2 3.39E-01 3.45E+00 1.33E+01
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> 29 2 -1.74E+00 3.11E+00 1.45E+01
>
> 30 2 -1.04E+00 3.25E+00 1.33E+01
>
> 31 2 -2.80E+00 2.15E+00 1.45E+01
>
> 32 2 -2.95E+00 1.51E+00 1.32E+01
>
> 33 2 -3.38E+00 -5.92E-01 1.44E+01
>
> 34 2 -3.27E+00 1.54E-01 1.32E+01
>
> 35 2 -2.76E+00 -1.88E+00 1.43E+01
>
> 36 2 -2.18E+00 -2.22E+00 1.31E+01
>
> 37 2 -2.83E-01 -3.23E+00 1.42E+01
>
> 38 2 -9.72E-01 -2.92E+00 1.30E+01
>
> 39 2 1.15E+00 -3.11E+00 1.43E+01
>
> 40 2 1.88E+00 -2.74E+00 1.31E+01
>
> 41 2 3.25E+00 -1.16E+00 1.43E+01
>
> 42 2 2.87E+00 -1.78E+00 1.31E+01
>
> 43 2 3.46E+00 1.37E-01 1.69E+01
>
> 44 2 3.40E+00 9.18E-01 1.57E+01
>
> 45 2 2.27E+00 2.68E+00 1.70E+01
>
> 46 2 2.80E+00 2.22E+00 1.57E+01
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> 47 2 1.03E+00 3.37E+00 1.70E+01
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> 48 2 3.16E-01 3.59E+00 1.58E+01
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> 49 2 -1.77E+00 3.03E+00 1.70E+01
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> 50 2 -1.11E+00 3.41E+00 1.58E+01
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> 51 2 -2.81E+00 2.06E+00 1.69E+01
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> 52 2 -3.20E+00 1.49E+00 1.57E+01
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> 53 2 -3.35E+00 -6.97E-01 1.68E+01
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> 54 2 -3.48E+00 8.14E-02 1.56E+01
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> 55 2 -2.74E+00 -1.99E+00 1.68E+01
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> 56 2 -2.26E+00 -2.48E+00 1.55E+01
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> 57 2 -2.84E-01 -3.34E+00 1.67E+01
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> 58 2 -9.95E-01 -3.15E+00 1.55E+01
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> 59 2 1.13E+00 -3.16E+00 1.67E+01
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> 60 2 1.81E+00 -2.83E+00 1.55E+01
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> 61 2 3.18E+00 -1.26E+00 1.68E+01
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> 62 2 2.86E+00 -1.86E+00 1.55E+01
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> 63 2 3.49E+00 2.37E-02 1.93E+01
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> 64 2 3.36E+00 7.97E-01 1.81E+01
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> 65 2 2.28E+00 2.59E+00 1.95E+01
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> 66 2 2.76E+00 2.09E+00 1.82E+01
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> 67 2 1.03E+00 3.29E+00 1.95E+01
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> 68 2 3.08E-01 3.45E+00 1.83E+01
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> 69 2 -1.79E+00 2.95E+00 1.95E+01
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> 70 2 -1.11E+00 3.28E+00 1.82E+01
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> 71 2 -2.84E+00 1.97E+00 1.94E+01
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> 72 2 -3.16E+00 1.37E+00 1.82E+01
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> 73 2 -3.37E+00 -8.10E-01 1.93E+01
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> 74 2 -3.43E+00 -2.93E-02 1.81E+01
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> 75 2 -2.76E+00 -2.11E+00 1.92E+01
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> 76 2 -2.24E+00 -2.57E+00 1.80E+01
>
> 77 2 -2.88E-01 -3.50E+00 1.92E+01
>
> 78 2 -9.94E-01 -3.26E+00 1.79E+01
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> 79 2 1.14E+00 -3.32E+00 1.92E+01
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> 80 2 1.78E+00 -2.92E+00 1.80E+01
>
> 81 2 3.21E+00 -1.39E+00 1.93E+01
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> 82 2 2.83E+00 -1.95E+00 1.80E+01
>
> 83 2 3.55E+00 -1.99E-01 2.17E+01
>
> 84 2 3.46E+00 7.34E-01 2.06E+01
>
> 85 2 2.24E+00 2.61E+00 2.18E+01
>
> 86 2 2.85E+00 2.02E+00 2.07E+01
>
> 87 2 1.15E+00 3.22E+00 2.18E+01
>
> 88 2 2.85E-01 3.45E+00 2.07E+01
>
> 89 2 -1.93E+00 2.86E+00 2.18E+01
>
> 90 2 -1.12E+00 3.29E+00 2.07E+01
>
> 91 2 -2.84E+00 2.01E+00 2.18E+01
>
> 92 2 -3.27E+00 1.28E+00 2.06E+01
>
> 93 2 -3.40E+00 -1.04E+00 2.16E+01
>
> 94 2 -3.53E+00 -1.13E-01 2.06E+01
>
> 95 2 -2.88E+00 -2.17E+00 2.16E+01
>
> 96 2 -2.29E+00 -2.78E+00 2.04E+01
>
> 97 2 -1.81E-01 -3.69E+00 2.15E+01
>
> 98 2 -1.05E+00 -3.48E+00 2.04E+01
>
> 99 2 1.06E+00 -3.54E+00 2.15E+01
>
> 100 2 1.86E+00 -3.12E+00 2.04E+01
>
> 101 2 3.32E+00 -1.42E+00 2.16E+01
>
> 102 2 2.90E+00 -2.15E+00 2.05E+01
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