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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1 by 1 by 1 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 = 0.0019815 secs
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read_data CPU = 0.0168803 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 = 0.000715256 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 = 103823 64000
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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) = 42.06 | 42.06 | 42.06 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 3563.3755 4630.6343 321.47655 -1067.2588 735.72049 604.78665 689.14827 -3277.411 815.58183 1306088.7 -1306723.8 17813.424 48631.318 503.827 0.0087118192
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100 3327.4724 4395.1107 305.12559 -1067.6382 597.93176 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.337 48631.318 478.20171 0.0075985539
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150 3036.9065 4740.2304 329.08513 -1703.3239 558.64983 619.91284 658.80687 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215188
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200 2697.958 4559.3445 316.52733 -1861.3864 522.09334 593.89129 754.61446 -3273.49 87.660461 1306183.9 -1306730 17888.936 48631.318 496.07143 0.0068706164
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250 2348.7568 4410.585 306.19988 -2061.8283 506.05007 575.35171 715.55054 -3276.3261 -18.364473 1306177.3 -1306741.4 11592.05 48631.318 479.88562 0.0071741032
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300 2019.8258 4040.1415 280.48226 -2020.3157 604.3077 641.66689 693.93801 -3278.5312 -115.73641 1306183.2 -1306749.1 3631.3628 48631.318 439.57995 0.0069886387
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350 1699.5166 3944.9851 273.87613 -2245.4685 452.07416 638.0653 658.79117 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22694 0.0062868111
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400 1399.2929 3726.098 258.68014 -2326.8051 457.91943 621.44726 639.39903 -3279.2395 -188.85914 1306185.4 -1306762.8 10792.274 48631.318 405.41134 0.0059340078
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450 1120.5249 3518.345 244.25712 -2397.8201 519.48856 584.65789 646.36689 -3278.6685 -289.59913 1306184.1 -1306764.2 2755.5598 48631.318 382.80716 0.0055707485
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500 868.0166 3359.8794 233.25583 -2491.8628 460.7393 581.49563 581.01731 -3281.5544 -252.20169 1306184.3 -1306765.7 6120.3639 48631.318 365.56528 0.0058756154
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550 637.01567 3214.9521 223.19441 -2577.9364 431.81483 578.87411 540.94047 -3281.5337 -266.36075 1306182.8 -1306764.5 8622.4334 48631.318 349.79661 0.0058589653
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600 418.04086 3113.4064 216.14472 -2695.3655 430.45935 538.68157 522.24598 -3283.456 -311.87901 1306174.3 -1306765.8 7068.9273 48631.318 338.74797 0.0059567598
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650 218.5966 2930.8439 203.47052 -2712.2473 514.47294 514.28379 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.553736 48631.318 318.88482 0.0052667842
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700 45.22721 2830.1443 196.47956 -2784.917 451.11156 498.26423 541.18835 -3282.1427 -375.95313 1306157.1 -1306774.4 3947.6276 48631.318 307.92741 0.0068019029
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750 -114.28621 2798.3153 194.26988 -2912.6016 412.753 503.2878 481.32173 -3284.3411 -393.53984 1306147 -1306779.1 7143.3414 48631.318 304.46466 0.0061596717
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800 -263.63817 2694.8084 187.08403 -2958.4466 455.67914 487.49754 476.8659 -3284.3133 -451.9578 1306145 -1306787.2 1185.9502 48631.318 293.20288 0.0058203332
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850 -397.71592 2559.1921 177.66902 -2956.9081 458.83317 481.2262 478.31241 -3284.068 -437.26503 1306138.6 -1306792.6 346.80209 48631.318 278.44745 0.0054921692
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900 -515.1823 2544.8753 176.67509 -3060.0576 395.00163 457.58988 446.68352 -3285.485 -423.56221 1306145 -1306795.3 3712.8598 48631.318 276.88864 0.0074054008
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950 -617.28259 2451.1723 170.16987 -3068.4549 383.64277 446.59877 434.4624 -3285.1348 -391.59344 1306142.3 -1306798.7 5429.2488 48631.318 266.69431 0.0057487316
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1000 -703.15534 2334.837 162.09342 -3037.9923 424.34948 462.21112 451.80809 -3284.3803 -426.53369 1306133.9 -1306799.3 1137.6145 48631.318 254.03675 0.0053914731
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1050 -771.1763 2303.837 159.94128 -3075.0133 426.21409 436.50718 435.09987 -3285.1939 -411.14054 1306125.6 -1306802.1 1636.9383 48631.318 250.66295 0.0069342505
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1100 -822.72236 2283.4196 158.52382 -3106.142 376.67684 447.77729 418.45768 -3286.5919 -377.48204 1306118.9 -1306803.8 4760.5163 48631.318 248.44119 0.0074025012
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1150 -857.06075 2259.0717 156.8335 -3116.1324 400.31523 431.65981 457.68066 -3285.1977 -430.47723 1306115.8 -1306805.9 3194.5161 48631.318 245.79223 0.007063589
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1200 -875.50848 2238.2637 155.38893 -3113.7722 445.38524 460.97125 432.10511 -3285.4238 -472.46606 1306114.7 -1306809 -653.49784 48631.318 243.52819 0.0071448738
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1250 -880.37572 2294.6889 159.30618 -3175.0646 411.35427 444.73793 420.06468 -3286.0366 -458.05371 1306104.4 -1306811.5 945.80793 48631.318 249.66481 0.011853487
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1300 -871.31064 2284.2298 158.58007 -3155.5405 404.97412 441.75285 426.34477 -3285.4859 -424.79609 1306094.9 -1306813.2 4406.6196 48631.318 248.48563 0.084424118
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1350 -816.70005 2325.9264 161.47481 -3142.6265 696.80296 442.50053 431.19923 -3285.7859 -450.2699 1305836.2 -1306813.3 593.8098 48631.318 251.40749 2.9297319
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1400 -794.25335 2263.5101 157.14163 -3057.7635 645.65165 466.22086 446.22268 -3285.1821 -420.65317 1305903.7 -1306813.8 1386.3633 48631.318 245.20554 1.8916154
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1450 -776.10866 2287.6575 158.81803 -3063.7661 427.03477 479.10627 439.67495 -3285.9537 -395.13186 1306087.6 -1306816.1 2936.7806 48631.318 248.87167 0.061343245
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1500 -725.48181 2371.413 164.63266 -3096.8948 390.03204 464.30903 446.91959 -3284.7809 -393.16613 1306095.4 -1306815.6 3544.25 48631.318 258.01286 0.011586563
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1550 -671.4904 2315.9297 160.7808 -2987.4201 457.04935 500.25282 464.76203 -3284.9311 -400.98103 1306091.7 -1306815.3 2052.6339 48631.318 251.97726 0.0094517862
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1600 -618.83633 2449.0918 170.02543 -3067.9281 425.47487 474.65876 471.99171 -3284.3677 -430.32107 1306091.3 -1306816.6 441.15682 48631.318 266.46311 0.014260935
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1650 -567.82245 2425.2238 168.36842 -2993.0462 421.01953 511.27133 463.22065 -3285.038 -377.24066 1306088.4 -1306814.7 5198.8565 48631.318 263.83185 0.074738268
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1700 -502.4486 2441.8554 169.52305 -2944.304 642.39962 512.90234 490.38297 -3283.9751 -417.39288 1305929.1 -1306817.7 1141.4411 48631.318 264.52393 2.043674
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1750 -459.52196 2499.0746 173.49543 -2958.5966 679.38259 505.31787 484.77659 -3284.6272 -384.27736 1305861.6 -1306820.8 1527.2046 48631.318 270.10074 3.1869342
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1800 -471.14403 2476.2266 171.90923 -2947.3706 442.47741 530.45656 474.03057 -3284.0954 -371.95117 1306084.3 -1306822.6 3392.2533 48631.318 269.36446 0.10416401
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1850 -462.80763 2536.7112 176.10831 -2999.5188 437.08241 525.07462 474.0838 -3283.7906 -422.23719 1306091.6 -1306821.3 1629.8629 48631.318 275.99502 0.016806806
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1900 -469.89289 2468.9765 171.4059 -2938.8694 446.77624 531.61059 496.01046 -3284.2338 -395.15325 1306085.7 -1306819.6 3119.5402 48631.318 268.62645 0.014601992
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1950 -491.08007 2445.5966 169.78278 -2936.6767 457.80452 527.23373 470.18125 -3283.9608 -391.86377 1306101.9 -1306818 1122.5275 48631.318 266.08018 0.018911601
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2000 -518.40811 2418.7208 167.91696 -2937.1289 415.93135 536.5973 480.44651 -3283.7881 -363.72783 1306096.2 -1306818.7 4475.7317 48631.318 263.09007 0.13504326
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Loop time of 70.696 on 1 procs for 2000 steps with 5500 atoms
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Performance: 1.222 ns/day, 19.638 hours/ns, 28.290 timesteps/s
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97.8% CPU use with 1 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 | 48.367 | 48.367 | 48.367 | 0.0 | 68.42
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Bond | 2.9191 | 2.9191 | 2.9191 | 0.0 | 4.13
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Kspace | 14.266 | 14.266 | 14.266 | 0.0 | 20.18
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Neigh | 1.5262 | 1.5262 | 1.5262 | 0.0 | 2.16
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Comm | 0.27841 | 0.27841 | 0.27841 | 0.0 | 0.39
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Output | 0.0035572 | 0.0035572 | 0.0035572 | 0.0 | 0.01
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Modify | 3.2856 | 3.2856 | 3.2856 | 0.0 | 4.65
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Other | | 0.05018 | | | 0.07
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Nlocal: 5500 ave 5500 max 5500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 15317 ave 15317 max 15317 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.30285e+06 ave 1.30285e+06 max 1.30285e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1302849
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Ave neighs/atom = 236.882
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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: 0:01:10
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