Simulation started.
exefile path: C:\Program Files\SpmSimulator\MD\
exefile name: mdafm
current path: C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/
Info: ForceField_Parameter -> C:\Program Files\SpmSimulator\MD\prm/mm3.prm
--Reading Simulation Parameter...
Info: tip file -> co.txyz
Info: mol file -> octane.txyz
Info: scanmode -> 1
Info: xy_scanning -> zigzag
Info: delta_X -> ignored
Info: delta_Y -> ignored
Info: delta_Z -> 0.5
Info: ScanArea w -> ignored
Info: ScanArea d -> ignored
Info: ScanArea h -> 6
Info: ThetaStepNumber -> ignored
Info: SamplingRange -> ignored
Info: TipZamplitude -> ignored
Info: SpringConst -> ignored
Info: FrequencyShift -> ignored
Info: tip_Position x -> 0
Info: tip_Position y -> 0
Info: tip_Position z -> 15
Info: TimeStep -> 1
Info: StepNumber -> 10,000
Info: Temperature -> 300
Info: ThreadNumber -> 1
Info: Cutoff -> on
Info: Cutoff_Distance -> 12
Info: PairList_Distance -> 13.5
Info: PairList_Update_freq -> 10
Info: PeriodicBoundaryCondition -> off
Info: RATTLE -> on
Info: Max_Iteration -> 500
Info: Rigid_Tolerance -> 1e-006
Info: Output_Directory -> .\
Info: Fx -> C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/MD_Fx.csv
Info: Fy -> C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/MD_Fy.csv
Info: Fz -> C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/MD_Fz.csv
Info: tipZ -> ignored
Info: FrequencyShift_1D -> ignored
Info: FrequencyShift -> ignored
Info: EnergyDissipation -> ignored
Info: Energy -> C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/MD_Energy.csv
Info: Movie file -> C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/MD_out.mvc
Info: movie_freq -> 50
Info: restart file_freq -> 1,000
--Reading parameter is finished.
Info: Number of atom C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/tipTemp.txyz -> 2
Info: Bond -> 1
Info: Angle -> 0
Info: Torsion -> 0
Info: Initial tip position -> 0, 0, 15
Info: Number of atom C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/sampleTemp.txyz -> 26
Info: Bond -> 25
Info: Angle -> 48
Info: Torsion -> 63
Info: velocity file -> none
--start getting vdW parameter.
Info: vdW parameter is set properly.
--start getting bond parameter.
Info: bond parameter is set properly.
--start getting dipole parameter.
warning: dipole parameter is not assigned.
Info: file name -> octane.txyz
   atom id (atom type) : 1 9 ( 1 5 )
   atom id (atom type) : 1 10 ( 1 5 )
   atom id (atom type) : 1 11 ( 1 5 )
   atom id (atom type) : 2 12 ( 1 5 )
   atom id (atom type) : 2 13 ( 1 5 )
   atom id (atom type) : 3 14 ( 1 5 )
   atom id (atom type) : 3 15 ( 1 5 )
   atom id (atom type) : 4 16 ( 1 5 )
   atom id (atom type) : 4 17 ( 1 5 )
   atom id (atom type) : 5 18 ( 1 5 )
   atom id (atom type) : 5 19 ( 1 5 )
   atom id (atom type) : 6 20 ( 1 5 )
   atom id (atom type) : 6 21 ( 1 5 )
   atom id (atom type) : 7 22 ( 1 5 )
   atom id (atom type) : 7 23 ( 1 5 )
   atom id (atom type) : 8 24 ( 1 5 )
   atom id (atom type) : 8 25 ( 1 5 )
   atom id (atom type) : 8 26 ( 1 5 )
--start getting angle parameter.
Info: angle parameter is set properly.
--start getting torsion parameter.

Info: torsion parameter is set properly.
Info: MM3 parameter setting is finished.
Info: pair list set -> 38
Info: vdW interaction set -> 29

--AFM simulation is start.

 Maximum Number of tip motion=      13



 1-th tip position:   0.0000 0.0000 15.0000
  Force_z = -0.16274522998729707

  progress = 7 %



 2-th tip position:   0.0000 0.0000 14.5000
  Force_z = -0.066398500094623114

  progress = 15 %



 3-th tip position:   0.0000 0.0000 14.0000
  Force_z = -0.18049817123970832

  progress = 23 %



 4-th tip position:   0.0000 0.0000 13.5000
  Force_z = -0.66966020375456747

  progress = 30 %



 5-th tip position:   0.0000 0.0000 13.0000
  Force_z = -0.30740524040381578

  progress = 38 %



 6-th tip position:   0.0000 0.0000 12.5000
  Force_z = -1.4432613034299615

  progress = 46 %



 7-th tip position:   0.0000 0.0000 12.0000
  Force_z = -1.4365618220253775

  progress = 53 %



 8-th tip position:   0.0000 0.0000 11.5000
  Force_z = -1.1050076104225317

  progress = 61 %



 9-th tip position:   0.0000 0.0000 11.0000
  Force_z = -1.6179413766556838

  progress = 69 %



 10-th tip position:   0.0000 0.0000 10.5000
  Force_z = 0.81488224832927991

  progress = 76 %



 11-th tip position:   0.0000 0.0000 10.0000
  Force_z = -3.8835576734204036

  progress = 84 %



 12-th tip position:   0.0000 0.0000 9.5000
  Force_z = 4.8729627672206641

  progress = 92 %



 13-th tip position:   0.0000 0.0000 9.0000
  Force_z = 28.143429557712597

  progress = 100 %


Info: making new file. -> C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/octane.txyz.fs1.txyz
Info: making new file. -> C:/Program Files/SpmSimulator/projects/MD/forcecurve_octane/forcecurve_octane.Restart.vel
CPU Time : 18.065 [second]
AFM Simulation is finished.



solver calculation finished.