forked from lijiext/lammps
263 lines
17 KiB
Groff
263 lines
17 KiB
Groff
LAMMPS (7 Aug 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
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using 1 OpenMP thread(s) per MPI task
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# 250 toluene system for drude polarizability example (Nose-Hoover)
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units real
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boundary p p p
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style opls
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improper_style fourier
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special_bonds lj/coul 0.0 0.0 0.5
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pair_style lj/cut/thole/long 2.600 8.0 8.0
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pair_modify mix geometric tail yes
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kspace_style pppm 1.0e-4
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read_data data.toluene extra/special/per/atom 1
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orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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5500 atoms
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scanning bonds ...
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4 = 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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8 = max dihedrals/atom
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scanning impropers ...
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2 = max impropers/atom
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reading bonds ...
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5500 bonds
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reading angles ...
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6000 angles
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reading dihedrals ...
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6000 dihedrals
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reading impropers ...
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1500 impropers
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5 = max # of 1-2 neighbors
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10 = max # of 1-3 neighbors
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16 = max # of 1-4 neighbors
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20 = max # of special neighbors
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special bonds CPU = 0.000718355 secs
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read_data CPU = 0.0167146 secs
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comm_modify vel yes
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group gTOLUENE molecule 1:250
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5500 atoms in group gTOLUENE
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group gCORES type 1 2 3 4 5 6 7
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3750 atoms in group gCORES
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group gDRUDES type 8 9 10 11 12
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1750 atoms in group gDRUDES
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pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
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pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
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pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
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pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
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pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
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pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
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pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
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pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
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pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
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pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
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pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
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pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
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pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
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pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
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pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
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pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
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pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
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pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
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pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
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pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
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pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
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pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
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pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
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pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
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pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
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pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
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pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
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pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
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pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
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pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
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pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
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pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
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pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
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pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
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pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
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pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
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pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
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pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
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pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
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pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
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pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
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pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
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pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
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pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
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pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
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pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
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pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
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pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
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pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
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pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
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pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
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pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
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pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
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pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
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pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
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pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
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pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
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pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
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pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
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pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
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pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
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pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
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pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
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pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
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pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
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pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
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pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
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pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
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neighbor 2.0 bin
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variable vTEMP equal 260.0
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variable vTEMP_D equal 1.0
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variable vPRESS equal 1.0
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velocity gCORES create ${vTEMP} 12345
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velocity gCORES create 260 12345
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velocity gDRUDES create ${vTEMP_D} 12345
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velocity gDRUDES create 1 12345
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fix fDRUDE all drude C C C C C N N D D D D D
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fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
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1250 = # of size 2 clusters
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0 = # of size 3 clusters
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250 = # of size 4 clusters
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0 = # of frozen angles
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find clusters CPU = 0.000344038 secs
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compute cTEMP_CORE gCORES temp/com
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compute cTEMP all temp/drude
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fix fDIRECT all drude/transform/direct
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fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
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fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
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fix fNVT1 gCORES nvt temp 260 260 100.0
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fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
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fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
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fix fNVT2 gDRUDES nvt temp 1 1 20.0
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fix fINVERSE all drude/transform/inverse
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fix fMOMENTUM all momentum 100 linear 1 1 1
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thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
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thermo 50
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timestep 0.5
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run 2000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
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G vector (1/distance) = 0.382011
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0325934
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estimated relative force accuracy = 9.8154e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 34263 16000
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Rebuild special list taking Drude particles into account
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Old max number of 1-2 to 1-4 neighbors: 19
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New max number of 1-2 to 1-4 neighbors: 20 (+1)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10
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ghost atom cutoff = 10
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binsize = 5, bins = 8 8 8
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/thole/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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Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
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Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
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0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
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50 3563.376 4630.6343 321.47655 -1067.2583 735.72048 604.78665 689.14826 -3277.411 815.58183 1306088.7 -1306723.8 17813.425 48631.318 503.827 0.0087118179
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100 3327.4722 4395.1107 305.12559 -1067.6385 597.93175 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.335 48631.318 478.2017 0.0075985638
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150 3036.9065 4740.2304 329.08513 -1703.3238 558.64983 619.91284 658.80686 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215227
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200 2697.9581 4559.3445 316.52734 -1861.3864 522.09335 593.8913 754.61446 -3273.49 87.660464 1306183.9 -1306730 17888.937 48631.318 496.07143 0.006870622
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250 2348.7563 4410.585 306.19988 -2061.8288 506.05006 575.35172 715.55055 -3276.3261 -18.364482 1306177.3 -1306741.4 11592.049 48631.318 479.88562 0.0071741023
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300 2019.8256 4040.1415 280.48225 -2020.3159 604.30771 641.66688 693.93802 -3278.5312 -115.73639 1306183.2 -1306749.1 3631.3625 48631.318 439.57995 0.0069886424
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350 1699.5169 3944.9851 273.87613 -2245.4682 452.07416 638.06529 658.79116 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22695 0.0062868216
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400 1399.2927 3726.098 258.68014 -2326.8053 457.91943 621.44727 639.39905 -3279.2395 -188.85912 1306185.4 -1306762.8 10792.273 48631.318 405.41133 0.0059340084
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450 1120.5246 3518.345 244.25712 -2397.8204 519.48859 584.6579 646.36688 -3278.6685 -289.59912 1306184.1 -1306764.2 2755.5597 48631.318 382.80717 0.005570751
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500 868.01643 3359.8794 233.25583 -2491.863 460.73928 581.49568 581.01732 -3281.5544 -252.20168 1306184.3 -1306765.7 6120.364 48631.318 365.56528 0.0058756204
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550 637.01646 3214.9521 223.19441 -2577.9356 431.81484 578.87415 540.94046 -3281.5337 -266.36074 1306182.8 -1306764.5 8622.4353 48631.318 349.79661 0.0058589476
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600 418.04028 3113.4063 216.14471 -2695.3661 430.45936 538.68158 522.24597 -3283.456 -311.87897 1306174.3 -1306765.8 7068.9275 48631.318 338.74796 0.0059567639
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650 218.59562 2930.8439 203.47052 -2712.2482 514.47296 514.2838 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.554086 48631.318 318.88481 0.0052667849
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700 45.227739 2830.1443 196.47957 -2784.9165 451.11157 498.26426 541.18833 -3282.1427 -375.95321 1306157.1 -1306774.4 3947.6268 48631.318 307.92741 0.0068018884
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750 -114.28676 2798.3154 194.26988 -2912.6022 412.75298 503.28782 481.32167 -3284.3411 -393.53987 1306147 -1306779.1 7143.3424 48631.318 304.46466 0.0061596613
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800 -263.63827 2694.8085 187.08403 -2958.4468 455.67916 487.49754 476.86576 -3284.3133 -451.95784 1306145 -1306787.2 1185.9474 48631.318 293.20289 0.0058203323
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850 -397.71592 2559.1922 177.66903 -2956.9082 458.83313 481.22619 478.31233 -3284.068 -437.26509 1306138.6 -1306792.6 346.80221 48631.318 278.44747 0.0054921238
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900 -515.18134 2544.8753 176.67509 -3060.0567 395.0016 457.5898 446.68361 -3285.485 -423.56234 1306145.1 -1306795.3 3712.8594 48631.318 276.88864 0.0074054726
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950 -617.28607 2451.1721 170.16985 -3068.4582 383.6428 446.59872 434.46241 -3285.1348 -391.59326 1306142.3 -1306798.7 5429.2191 48631.318 266.69429 0.0057487961
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1000 -703.15541 2334.8366 162.09339 -3037.992 424.34957 462.21115 451.80811 -3284.3803 -426.53346 1306133.9 -1306799.3 1137.6144 48631.318 254.03671 0.0053915025
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1050 -771.17572 2303.8364 159.94123 -3075.0121 426.21406 436.50744 435.10013 -3285.1938 -411.13999 1306125.6 -1306802.1 1636.9467 48631.318 250.66288 0.0069341736
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1100 -822.72317 2283.421 158.52392 -3106.1442 376.67703 447.77728 418.45763 -3286.5919 -377.48075 1306118.9 -1306803.8 4760.4718 48631.318 248.44134 0.0074024122
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1150 -857.06061 2259.0725 156.83355 -3116.1331 400.31517 431.65949 457.68078 -3285.1977 -430.47775 1306115.8 -1306805.9 3194.5159 48631.318 245.79231 0.007063706
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1200 -875.50971 2238.2632 155.38889 -3113.7729 445.38534 460.97161 432.10511 -3285.4238 -472.46582 1306114.7 -1306809 -653.49627 48631.318 243.52813 0.0071446561
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1250 -880.37609 2294.689 159.30619 -3175.0651 411.35498 444.73774 420.06429 -3286.0366 -458.05353 1306104.4 -1306811.5 945.79687 48631.318 249.66483 0.011854196
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1300 -871.31122 2284.2295 158.58005 -3155.5407 404.97869 441.75305 426.34479 -3285.4859 -424.79602 1306094.8 -1306813.2 4406.6128 48631.318 248.4856 0.084411062
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1350 -816.69657 2325.9211 161.47444 -3142.6176 696.85542 442.50059 431.19981 -3285.7859 -450.27129 1305836.1 -1306813.3 593.86622 48631.318 251.40736 2.9289249
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1400 -794.25213 2263.5122 157.14177 -3057.7643 645.6531 466.2204 446.22253 -3285.1821 -420.65316 1305903.7 -1306813.8 1386.3481 48631.318 245.20568 1.8917548
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1450 -776.1076 2287.6591 158.81814 -3063.7667 427.0331 479.10417 439.67675 -3285.9536 -395.13308 1306087.6 -1306816.1 2936.7117 48631.318 248.87185 0.061341392
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1500 -725.48032 2371.4108 164.63251 -3096.8911 390.03135 464.30817 446.91941 -3284.7808 -393.16302 1306095.4 -1306815.6 3544.3635 48631.318 258.01262 0.011585228
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1550 -671.48696 2315.9233 160.78035 -2987.4102 457.04771 500.26018 464.7623 -3284.931 -400.98142 1306091.7 -1306815.3 2052.6204 48631.318 251.97656 0.0094518433
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1600 -618.82679 2449.0893 170.02525 -3067.9161 425.47171 474.66369 471.99137 -3284.3677 -430.3224 1306091.3 -1306816.6 441.31257 48631.318 266.46283 0.014263201
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1650 -567.82233 2425.2281 168.36872 -2993.0504 421.02008 511.26686 463.22202 -3285.0378 -377.24205 1306088.4 -1306814.7 5198.6214 48631.318 263.83232 0.074728934
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1700 -502.46013 2441.8437 169.52224 -2944.3039 642.39863 512.90005 490.39655 -3283.975 -417.39351 1305929.1 -1306817.7 1141.2401 48631.318 264.52268 2.0436397
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1750 -459.52135 2499.0847 173.49613 -2958.606 679.34078 505.30943 484.78276 -3284.6269 -384.28217 1305861.7 -1306820.8 1527.0852 48631.318 270.10144 3.1876179
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1800 -471.14322 2476.2445 171.91047 -2947.3877 442.48278 530.4566 474.0343 -3284.0957 -371.97492 1306084.3 -1306822.6 3392.0306 48631.318 269.36641 0.1041603
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1850 -462.80151 2536.7173 176.10873 -2999.5188 437.07855 525.05914 474.07725 -3283.7908 -422.22641 1306091.6 -1306821.3 1630.1204 48631.318 275.99568 0.016808725
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1900 -469.8785 2468.9596 171.40473 -2938.8381 446.7879 531.6128 496.02681 -3284.2335 -395.17163 1306085.7 -1306819.6 3119.2384 48631.318 268.62462 0.014603394
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1950 -491.07182 2445.6794 169.78853 -2936.7512 457.80204 527.21208 470.1608 -3283.9622 -391.90163 1306101.9 -1306818 1122.0978 48631.318 266.08919 0.018903661
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2000 -518.41243 2418.604 167.90885 -2937.0165 415.92605 536.62844 480.48912 -3283.7876 -363.72641 1306096.2 -1306818.7 4474.8778 48631.318 263.07743 0.13492637
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Loop time of 22.3198 on 4 procs for 2000 steps with 5500 atoms
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Performance: 3.871 ns/day, 6.200 hours/ns, 89.606 timesteps/s
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98.3% 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 | 11.452 | 12.249 | 12.556 | 13.2 | 54.88
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Bond | 0.71352 | 0.72923 | 0.74557 | 1.3 | 3.27
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Kspace | 5.7189 | 6.0293 | 6.8195 | 18.6 | 27.01
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Neigh | 0.44028 | 0.44044 | 0.44065 | 0.0 | 1.97
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Comm | 0.39667 | 0.40817 | 0.41558 | 1.1 | 1.83
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Output | 0.0019479 | 0.0032187 | 0.0068657 | 3.7 | 0.01
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Modify | 2.413 | 2.4256 | 2.4347 | 0.5 | 10.87
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Other | | 0.0349 | | | 0.16
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Nlocal: 1375 ave 1407 max 1349 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Nghost: 8082.5 ave 8114 max 8047 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 325715 ave 343636 max 314954 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Total # of neighbors = 1302860
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Ave neighs/atom = 236.884
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Ave special neighs/atom = 15.6364
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Neighbor list builds = 44
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Dangerous builds = 0
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Total wall time: 0:00:22
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