[DFTB-Plus-User] DFTB+ 1.1 release candidate
Ran Friedman, Biochemisches Inst.
r.friedman at bioc.uzh.ch
Tue Apr 20 08:08:06 CEST 2010
> Hi,
>
> 10fs is probably too large a timestep. I would be cautious even with 1fs.
>Did you check energy/temperature conservation? Maybe you should study
>smaller systems or use approximate methods instead of increasing the
>timestep.
>
> Good luck,
> Ran
>
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Institute of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355559
> Skype: ran.friedman
> ------------------------------------------------------
>
>
> On Tue, 20 Apr 2010 10:49:43 +0800
> Jiatao Sun <sunjiatao at gmail.com> wrote:
>> Dear members,
>>
>> I am doing Berendsen thermostat MD simulation in NVT ensemble on nano
>> systems by Snapshot 081217 version.
>> The Steps is 10000.
>> The Timestep keyword is initially 1fs. The program terminated normally.
>>The
>> timestep 5fs is ok as well.
>> When the Timestep is changed to 10fs or larger femtosecond, it exits
>> abnormally with an error message "Failure in diagonalisation routine
>>zhegvd,
>> non-positive definite overlap! Minor 97 responsible." The number " 97
>>"
>> will change depending on the timestep. Also the program exist at different
>> geometry steps depending on the different system and different Step and
>> Timestep.
>> I have also tried other similar nano-systems. The error messages still
>>occur
>> for other systems when set larger Steps (e.g. 10000) and slightly larger
>> Timestep.
>> It seems that 1fs timestep is the most stable without any error message.
>> However 1fs is not suitable for very large system due to the very
>> time-consuming.
>> I have googled this error message. But have no clear solution. Any
>> suggestion will be much appreciated.
>>
>>
>> Here are the input files.
>>
>> Geometry = GenFormat {
>> <<< "POSCAR"
>> }
>> Hamiltonian = DFTB {
>> SCC = No
>> # SCCTolerance = 1e-5
>> # MaxSCCIterations = 100
>> MaxAngularMomentum = {
>> # Ga = "d"; As = "d"
>> C = "p"
>> }
>> # PolynomialRepulsive = {}
>> OrbitalResolvedSCC = No
>> OldSKInterpolation = No
>> SpinPolarisation = {}
>> Eigensolver = DivideAndConquer {}
>> OrbitalPotential = {}
>> Dispersion = {}
>> # Parametrization files
>> SlaterKosterFiles = Type2FileNames {
>> Prefix = "./mio-0-1/"
>> Separator = "-"
>> Suffix = ".skf"
>> LowerCaseTypeName = Yes
>> }
>> # K-points sampling in the BZ
>> # KPointsAndWeights = SupercellFolding {
>> KPointsAndWeights = {
>> 0.00000000000000 0.00000000000000 0.00000000000000 1
>> 0.00000000000000 0.04166666666667 0.00000000000000 2
>> 0.00000000000000 0.08333333333333 0.00000000000000 2
>> 0.00000000000000 0.12500000000000 0.00000000000000 2
>> 0.00000000000000 0.16666666666667 0.00000000000000 2
>> 0.00000000000000 0.20833333333333 0.00000000000000 2
>> 0.00000000000000 0.25000000000000 0.00000000000000 2
>> 0.00000000000000 0.29166666666667 0.00000000000000 2
>> 0.00000000000000 0.33333333333333 0.00000000000000 2
>> 0.00000000000000 0.37500000000000 0.00000000000000 2
>> 0.00000000000000 0.41666666666667 0.00000000000000 2
>> 0.00000000000000 0.45833333333333 0.00000000000000 2
>> 0.00000000000000 0.50000000000000 0.00000000000000 1
>> }
>> }
>> #Additional optional definitions
>> ParserOptions = {
>> ParserVersion = 3
>> WriteHSDInput = Yes
>> WriteXMLInput = No
>> StopAfterParsing = No
>> IgnoreUnprocessedNodes = No
>> }
>> Driver = VelocityVerlet {
>> TimeStep [Femtosecond] = 20.0
>> MovedAtoms = Range { 1 -1 }
>> Steps = 10000
>> Thermostat = Berendsen {
>> CouplingStrength = 0.1
>> AdaptFillingTemp = Yes
>> Temperature [Kelvin] = 300
>> }
>> OutputPrefix = "md"
>> MDRestartFrequency = 100
>> }
>>
>> Options = {
>> # MullikenAnalysis = No
>> # CalculateForces = Yes
>> WriteEigenvectors = No
>> WriteAutotestTag = No
>> WriteDetailedXML = No
>> WriteResultsTag = No
>> WriteDetailedOut = Yes
>> WriteBandOut = Yes
>> AtomResolvedEnergies = No
>> # RestartFrequency = 20
>> RandomSeed = 0
>> WriteHS = No
>> WriteRealHS = No
>> MinimiseMemoryUsage = No
>> }
>>
>> POSCAR
>>
>> 16 F
>> C
>> 1 1 0.33333 0.00000 0.25000
>> 2 1 0.41667 0.00000 0.25000
>> 3 1 0.50000 0.00000 0.25000
>> 4 1 0.58333 0.00000 0.25000
>> 5 1 0.34722 0.50000 0.25000
>> 6 1 0.43056 0.50000 0.25000
>> 7 1 0.51389 0.50000 0.25000
>> 8 1 0.59722 0.50000 0.25000
>> 9 1 0.37500 0.50000 0.25000
>> 10 1 0.45833 0.50000 0.25000
>> 11 1 0.54167 0.50000 0.25000
>> 12 1 0.62500 0.50000 0.25000
>> 13 1 0.38889 0.00000 0.25000
>> 14 1 0.47222 0.00000 0.25000
>> 15 1 0.55555 0.00000 0.25000
>> 16 1 0.63889 0.00000 0.25000
>> 0.00000000 0.00000000 0.00000000
>> 51.3681859436258 0 0
>> 0 2.47138050151 0
>> 0 0 15
>>
>>
>>
>>
>>
>>
>> On Thu, Apr 8, 2010 at 2:53 PM, Bálint Aradi <
>> balint.aradi at bccms.uni-bremen.de> wrote:
>>
>>> Dear List members,
>>>
>>> thank you very much for taking part in the activity of the
>>> DFTB+ community. Your contributions help inexperienced users to make
>>> their first steps with DFTB+, experienced users to find answers to their
>>> specific questions, and of course your feedback helps us developers
>>> to understand which parts of the code and tools need improvement and
>>> which features are needed by the community.
>>>
>>> As sign of our appreciation, and in order to encourage you to continue
>>> your active participation in the future, we would like to invite you to
>>> try the release candidate for the next DFTB+ release (1.1) before its
>>> official announcment. (The official 1.1 version should be released in
>>> ca. 5 weeks.)
>>>
>>> You can download the soucre, precompiled binaries, the autotest and
>>> the manual from the website as usual. You will also find a list of the
>>> major changes under
>>>
>>> http://www.dftb-plus.info/about_dftb/release_11/
>>>
>>> If you have any comments or suggestions regarding the new version, or
>>> if you think you having found a bug, please do not hesitate to contact us.
>>>
>>> We hope, that you'll find our new release useful.
>>>
>>>
>>> Best regards
>>>
>>> The DFTB+ developer team
>>>
>>> --
>>> Dr. Bálint Aradi
>>> Bremen Center for Computational Materials Science, University of Bremen
>>> http://www.bccms.uni-bremen.de/en/~b_aradi<http://www.bccms.uni-bremen.de/en/%7Eb_aradi>
>>>
>>>
>>>
>>> _______________________________________________
>>> DFTB-Plus-User mailing list
>>> DFTB-Plus-User at dftb-plus.info
>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>>
>>>
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Institute of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Skype: ran.friedman
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