You need to establish the MD.NoseMass parameter by hand. Likely, the default value is too large for carbon.
-Salvador ________________________________ From: [email protected] <[email protected]> on behalf of Younas Khan <[email protected]> Sent: Wednesday, June 1, 2016 10:12 AM To: siesta-l Subject: Re: [SIESTA-L] MD simulation This is a typical MD problem in SIESTA. It has been discussed several time here. Kindly go through the old threads, you will find an answer. Best of Luck. [https://ipmcdn.avast.com/images/2016/icons/icon-envelope-tick-round-orange_184x116-v1.png]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avast.com_sig-2Demail-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail-26utm-5Fterm-3Dicon&d=CwMFaQ&c=JL-fUnQvtjNLb7dA39cQUcqmjBVITE8MbOdX7Lx6ge8&r=n_Y76F1vumEs9EYNHN2gzA5FD9jzyPhrzl3eOzxCHIQ&m=gXIPcy4EVE_H5nOwx0CXvviPrB4WQfli6Q2a64AEDzQ&s=zsFyFdSv9oGG_e9D_sPAIOHt5K3tlnBiyaWwsWfZlXM&e=> Virus-free. www.avast.com<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avast.com_sig-2Demail-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail-26utm-5Fterm-3Dlink&d=CwMFaQ&c=JL-fUnQvtjNLb7dA39cQUcqmjBVITE8MbOdX7Lx6ge8&r=n_Y76F1vumEs9EYNHN2gzA5FD9jzyPhrzl3eOzxCHIQ&m=gXIPcy4EVE_H5nOwx0CXvviPrB4WQfli6Q2a64AEDzQ&s=DX4NxBfQPFnRcFyE6rr_y6aE1GNjIpIxpM31XhCUAbg&e=> On Wed, Jun 1, 2016 at 6:25 PM, ZARA NBSH <[email protected]<mailto:[email protected]>> wrote: Dear all, I am new in siesta and would like to perform molecular dynamics calculation on graphene sheet with periodic boundary conditions and the total number of C atoms 200. I set the temperature to 300K, but in the output the temperature fluctuations are very large between 230 to 360 K. I copy the input file here. Would any one help me what is wrong in my calculations? # fdf file SystemName graphene SystemLabel c NumberOfAtoms 200 NumberOfSpecies 1 %block ChemicalSpeciesLabel 1 6 C %endblock ChemicalSpeciesLabel XC.functional GGA XC.authors PBE LatticeConstant 2.471763457 Ang %block LatticeParameters 10 8.66025404 8 90. 90. 90. %endblock LatticeParameters AtomicCoordinatesFormat Ang AtomicCoordinatesAndAtomicSpecies < xyz %block kgrid_Monkhorst_Pack 1 0 0 0.0 0 1 0 0.0 0 0 1 0.0 %endblock kgrid_Monkhorst_Pack MeshCutoff 300.0 Ry # SCF options MaxSCFIterations 100 # Maximum number of SCF iter DM.NumberPulay 3 # One Pulay every 3 iter DM.MixingWeight 0.25 # New DM amount for next SCF cycle DM.Tolerance 5.d-4 # Tolerance in maximum difference SolutionMethod diagon # OrderN or Diagon ElectronicTemperature 25 meV # Temp. for Fermi smearing # structural infomation AtomCoorFormatOut Ang WriteCoorXmol T WriteMDXmol T WriteForces T # options for MD MD.MaxForceTol 0.01 eV/Ang MD.TypeOfRun Nose MD.VariableCell T MD.NumCGSteps 400 MD.Broyden.History.Steps 6 MD.Broyden.Initial.Inverse.Jacobian 1.0 MD.InitialTimeStep 1 MD.FinalTimeStep 2000 MD.LengthTimeStep 1 fs MD.InitialTemperature 300 K MD.TargetTemperature 300 K MD.AnnealOption TemperatureAndPressure MD.TauRelax 100.0 fs
