forked from lijiext/lammps
630 lines
28 KiB
Groff
630 lines
28 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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84 atoms in group peptide
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group one id 2 4 5 6
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4 atoms in group one
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group two id 80 82 83 84
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4 atoms in group two
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group ref id 37
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1 atoms in group ref
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group colvar union one two ref
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9 atoms in group colvar
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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shell "rm -f out*.colvars.*"
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fix 2 all colvars peptide.colvars
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fix 2a ref setforce 0.0 0.0 0.0
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 4312 960
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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colvars: Creating proxy instance
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2018-11-16.
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colvars: Please cite Fiorin et al, Mol Phys 2013:
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colvars: http://dx.doi.org/10.1080/00268976.2013.813594
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colvars: in any publication based on this calculation.
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colvars: SMP parallelism is available.
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colvars: Using LAMMPS interface, version 2018-08-29.
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colvars: ----------------------------------------------------------------------
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colvars: Reading new configuration from file "peptide.colvars":
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colvars: # smp = on [default]
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 1000
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colvars: # scriptedColvarForces = off [default]
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colvars: # scriptingAfterBiases = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = "one"
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colvars: Initializing a new "distance" component.
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colvars: # name = "" [default]
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # scalable = on [default]
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colvars: Initializing atom group "group1".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
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colvars: Initializing atom group "group2".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
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colvars: # oneSiteSystemForce = off [default]
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colvars: # oneSiteTotalForce = off [default]
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colvars: All components initialized.
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colvars: # timeStepFactor = 1 [default]
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputTotalForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: # subtractAppliedForce = off [default]
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colvars: # runAve = off [default]
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colvars: # corrFunc = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = "two"
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colvars: Initializing a new "distance" component.
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colvars: # name = "" [default]
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # scalable = on [default]
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colvars: Initializing atom group "group1".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
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colvars: Initializing atom group "group2".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
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colvars: # oneSiteSystemForce = off [default]
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colvars: # oneSiteTotalForce = off [default]
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colvars: All components initialized.
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colvars: # timeStepFactor = 1 [default]
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputTotalForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: # subtractAppliedForce = off [default]
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colvars: # runAve = off [default]
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colvars: # corrFunc = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables initialized, 2 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new "harmonic" instance.
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colvars: # name = "h_pot"
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colvars: # colvars = { one, two }
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colvars: # outputEnergy = off [default]
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colvars: # timeStepFactor = 1 [default]
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colvars: # writeTISamples = off [default]
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colvars: # writeTIPMF = off [default]
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colvars: # centers = { 10, 10 }
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colvars: # targetCenters = { 10, 10 } [default]
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colvars: # outputCenters = off [default]
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colvars: # forceConstant = 100
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colvars: # targetForceConstant = -1 [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables biases initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables module (re)initialized.
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colvars: ----------------------------------------------------------------------
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colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
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colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
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colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
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colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
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colvars: The restart output state file will be "rest.colvars.state".
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colvars: The final output state file will be "out.colvars.state".
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colvars: Writing to colvar trajectory file "out.colvars.traj".
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colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
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colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
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colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
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colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
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colvars: Performing analysis.
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond f_2
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
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10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
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20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
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30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
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40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
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50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
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60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
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70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
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80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
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90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
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SHAKE stats (type/ave/delta) on step 100
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4 1.11098 8.97155e-05
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6 0.996996 1.00568e-05
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8 1.08 6.02345e-06
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10 1.111 1.84253e-05
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12 1.08 7.2713e-06
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14 0.959996 0
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18 0.957198 3.36079e-05
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31 104.52 0.0030599
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100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
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colvars: Saving collective variables state to "out.colvars.state".
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Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
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Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s
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98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52
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Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19
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Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83
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Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48
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Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58
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Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06
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Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16
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Other | | 0.001141 | | | 0.19
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Nlocal: 501 ave 513 max 489 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Nghost: 6563.25 ave 6596 max 6519 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Neighs: 177059 ave 181742 max 172942 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Total # of neighbors = 708237
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Ave neighs/atom = 353.412
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 12
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Dangerous builds = 2
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 4312 960
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colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
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colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
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colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
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colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
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SHAKE stats (type/ave/delta) on step 100
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4 1.11098 8.97155e-05
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6 0.996996 1.00568e-05
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8 1.08 6.02345e-06
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10 1.111 1.84253e-05
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12 1.08 7.2713e-06
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14 0.959996 0
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18 0.957198 3.36079e-05
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31 104.52 0.0030599
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Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond f_2
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100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
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110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
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120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
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130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
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140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
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150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
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160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
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170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217
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180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037
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190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 1.81266e-06
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6 0.997 7.79424e-07
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8 1.08 1.08903e-06
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10 1.111 2.96503e-07
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12 1.08 4.69038e-07
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14 0.960001 0
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18 0.957201 3.76471e-06
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31 104.52 0.000411055
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200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
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colvars: Saving collective variables state to "out.colvars.state".
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Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
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Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s
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98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50
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Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20
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Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23
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Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84
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Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48
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Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08
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Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38
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Other | | 0.001623 | | | 0.28
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Nlocal: 501 ave 513 max 481 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 6556.5 ave 6608 max 6514 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 177021 ave 182259 max 172089 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Total # of neighbors = 708083
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Ave neighs/atom = 353.335
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 7
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Dangerous builds = 0
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fix 2 all colvars peptide.colvars input out.colvars.state output out2
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colvars: Resetting the Collective Variables module.
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.0228209
|
|
estimated relative force accuracy = 6.87243e-05
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 4312 960
|
|
colvars: Creating proxy instance
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Initializing the collective variables module, version 2018-11-16.
|
|
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
|
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
|
colvars: in any publication based on this calculation.
|
|
colvars: SMP parallelism is available.
|
|
colvars: Using LAMMPS interface, version 2018-08-29.
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Reading new configuration from file "peptide.colvars":
|
|
colvars: # smp = on [default]
|
|
colvars: # colvarsTrajFrequency = 1
|
|
colvars: # colvarsRestartFrequency = 1000
|
|
colvars: # scriptedColvarForces = off [default]
|
|
colvars: # scriptingAfterBiases = off [default]
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Initializing a new collective variable.
|
|
colvars: # name = "one"
|
|
colvars: Initializing a new "distance" component.
|
|
colvars: # name = "" [default]
|
|
colvars: # componentCoeff = 1 [default]
|
|
colvars: # componentExp = 1 [default]
|
|
colvars: # period = 0 [default]
|
|
colvars: # wrapAround = 0 [default]
|
|
colvars: # forceNoPBC = off [default]
|
|
colvars: # scalable = on [default]
|
|
colvars: Initializing atom group "group1".
|
|
colvars: # name = "" [default]
|
|
colvars: # centerReference = off [default]
|
|
colvars: # rotateReference = off [default]
|
|
colvars: # atomsOfGroup = "" [default]
|
|
colvars: # indexGroup = "" [default]
|
|
colvars: # psfSegID = [default]
|
|
colvars: # atomsFile = "" [default]
|
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
colvars: # enableForces = on [default]
|
|
colvars: # enableFitGradients = on [default]
|
|
colvars: # printAtomIDs = off [default]
|
|
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
colvars: Initializing atom group "group2".
|
|
colvars: # name = "" [default]
|
|
colvars: # centerReference = off [default]
|
|
colvars: # rotateReference = off [default]
|
|
colvars: # atomsOfGroup = "" [default]
|
|
colvars: # indexGroup = "" [default]
|
|
colvars: # psfSegID = [default]
|
|
colvars: # atomsFile = "" [default]
|
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
colvars: # enableForces = on [default]
|
|
colvars: # enableFitGradients = on [default]
|
|
colvars: # printAtomIDs = off [default]
|
|
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
colvars: # oneSiteSystemForce = off [default]
|
|
colvars: # oneSiteTotalForce = off [default]
|
|
colvars: All components initialized.
|
|
colvars: # timeStepFactor = 1 [default]
|
|
colvars: # width = 1 [default]
|
|
colvars: # lowerBoundary = 0 [default]
|
|
colvars: # upperBoundary = 0 [default]
|
|
colvars: # expandBoundaries = off [default]
|
|
colvars: # extendedLagrangian = off [default]
|
|
colvars: # outputValue = on [default]
|
|
colvars: # outputVelocity = off [default]
|
|
colvars: # outputTotalForce = off [default]
|
|
colvars: # outputAppliedForce = off [default]
|
|
colvars: # subtractAppliedForce = off [default]
|
|
colvars: # runAve = off [default]
|
|
colvars: # corrFunc = off [default]
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Initializing a new collective variable.
|
|
colvars: # name = "two"
|
|
colvars: Initializing a new "distance" component.
|
|
colvars: # name = "" [default]
|
|
colvars: # componentCoeff = 1 [default]
|
|
colvars: # componentExp = 1 [default]
|
|
colvars: # period = 0 [default]
|
|
colvars: # wrapAround = 0 [default]
|
|
colvars: # forceNoPBC = off [default]
|
|
colvars: # scalable = on [default]
|
|
colvars: Initializing atom group "group1".
|
|
colvars: # name = "" [default]
|
|
colvars: # centerReference = off [default]
|
|
colvars: # rotateReference = off [default]
|
|
colvars: # atomsOfGroup = "" [default]
|
|
colvars: # indexGroup = "" [default]
|
|
colvars: # psfSegID = [default]
|
|
colvars: # atomsFile = "" [default]
|
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
colvars: # enableForces = on [default]
|
|
colvars: # enableFitGradients = on [default]
|
|
colvars: # printAtomIDs = off [default]
|
|
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
|
colvars: Initializing atom group "group2".
|
|
colvars: # name = "" [default]
|
|
colvars: # centerReference = off [default]
|
|
colvars: # rotateReference = off [default]
|
|
colvars: # atomsOfGroup = "" [default]
|
|
colvars: # indexGroup = "" [default]
|
|
colvars: # psfSegID = [default]
|
|
colvars: # atomsFile = "" [default]
|
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
|
colvars: # enableForces = on [default]
|
|
colvars: # enableFitGradients = on [default]
|
|
colvars: # printAtomIDs = off [default]
|
|
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
|
colvars: # oneSiteSystemForce = off [default]
|
|
colvars: # oneSiteTotalForce = off [default]
|
|
colvars: All components initialized.
|
|
colvars: # timeStepFactor = 1 [default]
|
|
colvars: # width = 1 [default]
|
|
colvars: # lowerBoundary = 0 [default]
|
|
colvars: # upperBoundary = 0 [default]
|
|
colvars: # expandBoundaries = off [default]
|
|
colvars: # extendedLagrangian = off [default]
|
|
colvars: # outputValue = on [default]
|
|
colvars: # outputVelocity = off [default]
|
|
colvars: # outputTotalForce = off [default]
|
|
colvars: # outputAppliedForce = off [default]
|
|
colvars: # subtractAppliedForce = off [default]
|
|
colvars: # runAve = off [default]
|
|
colvars: # corrFunc = off [default]
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Collective variables initialized, 2 in total.
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Initializing a new "harmonic" instance.
|
|
colvars: # name = "h_pot"
|
|
colvars: # colvars = { one, two }
|
|
colvars: # outputEnergy = off [default]
|
|
colvars: # timeStepFactor = 1 [default]
|
|
colvars: # writeTISamples = off [default]
|
|
colvars: # writeTIPMF = off [default]
|
|
colvars: # centers = { 10, 10 }
|
|
colvars: # targetCenters = { 10, 10 } [default]
|
|
colvars: # outputCenters = off [default]
|
|
colvars: # forceConstant = 100
|
|
colvars: # targetForceConstant = -1 [default]
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Collective variables biases initialized, 1 in total.
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Collective variables module (re)initialized.
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
|
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
|
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
|
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: Restarting from file "out.colvars.state".
|
|
colvars: Restarting collective variable "one" from value: 10.0128
|
|
colvars: Restarting collective variable "two" from value: 9.62236
|
|
colvars: ----------------------------------------------------------------------
|
|
colvars: The restart output state file will be "rest.colvars.state".
|
|
colvars: The final output state file will be "out2.colvars.state".
|
|
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
|
colvars: Setting initial step number from LAMMPS: 200
|
|
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
|
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
|
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
|
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
|
colvars: Performing analysis.
|
|
SHAKE stats (type/ave/delta) on step 200
|
|
4 1.111 1.81266e-06
|
|
6 0.997 7.79424e-07
|
|
8 1.08 1.08903e-06
|
|
10 1.111 2.96503e-07
|
|
12 1.08 4.69038e-07
|
|
14 0.960001 0
|
|
18 0.957201 3.76471e-06
|
|
31 104.52 0.000411055
|
|
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
|
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
|
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
|
210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486
|
|
220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368
|
|
230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541
|
|
240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818
|
|
250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013
|
|
260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096
|
|
270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131
|
|
280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488
|
|
290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135
|
|
SHAKE stats (type/ave/delta) on step 300
|
|
4 1.111 1.79792e-05
|
|
6 0.997005 1.02512e-05
|
|
8 1.08 1.85102e-05
|
|
10 1.111 9.98838e-06
|
|
12 1.08 8.84113e-06
|
|
14 0.960008 0
|
|
18 0.957203 1.8445e-05
|
|
31 104.52 0.00168382
|
|
300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246
|
|
colvars: Saving collective variables state to "out2.colvars.state".
|
|
Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
|
|
|
|
Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s
|
|
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60
|
|
Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20
|
|
Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99
|
|
Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05
|
|
Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39
|
|
Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09
|
|
Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40
|
|
Other | | 0.001705 | | | 0.29
|
|
|
|
Nlocal: 501 ave 513 max 472 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
|
Nghost: 6612.75 ave 6681 max 6561 min
|
|
Histogram: 1 1 0 0 0 1 0 0 0 1
|
|
Neighs: 177038 ave 180136 max 170218 min
|
|
Histogram: 1 0 0 0 0 0 0 1 0 2
|
|
|
|
Total # of neighbors = 708152
|
|
Ave neighs/atom = 353.369
|
|
Ave special neighs/atom = 2.34032
|
|
Neighbor list builds = 8
|
|
Dangerous builds = 0
|
|
|
|
colvars: Resetting the Collective Variables module.
|
|
|
|
Please see the log.cite file for references relevant to this simulation
|
|
|
|
Total wall time: 0:00:01
|