forked from lijiext/lammps
336 lines
12 KiB
Plaintext
336 lines
12 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units metal
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atom_style atomic
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atom_modify map hash
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boundary p p p
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variable l equal 3
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variable l2 equal 0.5*$l
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variable l2 equal 0.5*3
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variable L equal 10
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variable L2 equal 0.5*$L
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variable L2 equal 0.5*10
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variable h equal $L
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variable h equal 10
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lattice fcc 4.08 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 4.08 4.08 4.08
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region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
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region BOX block -1.5 ${l2} -${L2} ${L2} -${l2} ${l2}
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region BOX block -1.5 1.5 -${L2} ${L2} -${l2} ${l2}
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region BOX block -1.5 1.5 -5 ${L2} -${l2} ${l2}
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region BOX block -1.5 1.5 -5 5 -${l2} ${l2}
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region BOX block -1.5 1.5 -5 5 -1.5 ${l2}
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region BOX block -1.5 1.5 -5 5 -1.5 1.5
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create_box 1 BOX
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Created orthogonal box = (-6.12 -20.4 -6.12) to (6.12 20.4 6.12)
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1 by 4 by 1 MPI processor grid
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create_atoms 1 region BOX
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Created 360 atoms
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pair_style eam
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pair_coeff * * Au_u3.eam
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mass * 196.97
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### NOTE change to CB -linear
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fix PP all atc field Au_elastic.mat
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ATC: constructing shape function field estimate with parameter file Au_elastic.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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fix_modify PP mesh create 1 $h 1 BOX p f p
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fix_modify PP mesh create 1 10 1 BOX p f p
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ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements
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fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
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fix_modify PP gradients add displacement
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fix_modify PP set reference_potential_energy
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fix_modify PP output counter step
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fix_modify PP output eam_energyPP 1 text
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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fix ATC all atc elastic Au_elastic.mat
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ATC: constructing elastic coupling with parameter file Au_elastic.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: computed mass density : 11.6006
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ATC: computed mass density : 11.6006
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ATC: 2 materials defined from Au_elastic.mat
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fix_modify ATC mesh create 1 $h 1 BOX p f p
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fix_modify ATC mesh create 1 10 1 BOX p f p
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ATC: created uniform mesh with 44 nodes, 11 unique nodes, and 10 elements
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fix_modify ATC internal_quadrature off
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fix_modify ATC control momentum none
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#fix_modify ATC consistent_fe_initialization on
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fix_modify ATC output counter step
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fix_modify ATC output eam_energyFE 1 text binary
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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fix_modify ATC material all Au_cubic
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dump CONFIG all custom 1 eam_energy.dmp id type x y z
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thermo 1
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timestep 0 # 1.e-20 # 0
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variable e0 equal pe
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variable L0 equal ly
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run 0
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Setting up run ...
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ATC: CB stiffness: 11.5362 Einstein freq: 4682.34
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ATC: CB stiffness: 11.5362 Einstein freq: 4682.34
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ATC: WARNING: all initial conditions for displacement have not been defined and the undefined are assumed zero
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ATC: WARNING: all initial conditions for velocity have not been defined and the undefined are assumed zero
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Memory usage per processor = 41.8034 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -1414.8 0 -1414.8 0.022463201
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Loop time of 1.0252e-05 on 4 procs for 0 steps with 360 atoms
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Pair time (%) = 0 (0)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0 (0)
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Outpt time (%) = 0 (0)
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Other time (%) = 1.0252e-05 (100)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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variable pe equal pe-${e0}
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variable pe equal pe--1414.8000000636002369
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variable dL equal ly-${L0}
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variable dL equal ly-40.799999999999997158
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variable strain equal v_dL/${L0}
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variable strain equal v_dL/40.799999999999997158
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variable x equal y[1]
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variable x2 equal y[2]
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variable v equal vy[1]
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thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain
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thermo_modify format 2 %15.8g
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###############################################################################
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log eam_energy.log
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run 1
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Setting up run ...
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Memory usage per processor = 41.8034 Mbytes
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Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
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0 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0
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1 -1414.8 0 0 0 0 -19.38 0 -19.38 40.8 0 0
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Loop time of 0.00549316 on 4 procs for 1 steps with 360 atoms
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Pair time (%) = 0.000414193 (7.54015)
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Neigh time (%) = 0 (0)
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Comm time (%) = 6.98566e-05 (1.2717)
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Outpt time (%) = 0.0019924 (36.2706)
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Other time (%) = 0.00301671 (54.9175)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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velocity all set 0 0.1 0 units box
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fix_modify ATC fix velocity y all 0.1
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run 1
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Setting up run ...
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Memory usage per processor = 41.8034 Mbytes
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Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
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1 -1414.7633 0 0.036746101 0 0 -19.38 0.1 -19.38 40.8 0 0
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2 -1414.7633 0 0.036746101 0.036746101 0 -19.38 0.1 -19.38 40.8 0 0
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Loop time of 0.00695777 on 4 procs for 1 steps with 360 atoms
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Pair time (%) = 0.000445962 (6.40955)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000112355 (1.61481)
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Outpt time (%) = 0.00171965 (24.7156)
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Other time (%) = 0.0046798 (67.26)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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velocity all set 0 0.2 0 units box
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fix_modify ATC fix velocity y all 0.2
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run 1
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Setting up run ...
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Memory usage per processor = 41.8034 Mbytes
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Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
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2 -1414.653 0 0.1469844 0.036746101 0 -19.38 0.2 -19.38 40.8 0 0
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3 -1414.653 0 0.1469844 0.1469844 0 -19.38 0.2 -19.38 40.8 0 0
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Loop time of 0.00692767 on 4 procs for 1 steps with 360 atoms
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Pair time (%) = 0.000420749 (6.07346)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000110626 (1.59688)
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Outpt time (%) = 0.00177026 (25.5534)
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Other time (%) = 0.00462604 (66.7762)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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velocity all set 0 0.3 0 units box
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fix_modify ATC fix velocity y all 0.3
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run 1
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Setting up run ...
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Memory usage per processor = 41.8034 Mbytes
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Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
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3 -1414.4693 0 0.33071491 0.1469844 0 -19.38 0.3 -19.38 40.8 0 0
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4 -1414.4693 0 0.33071491 0.33071491 0 -19.38 0.3 -19.38 40.8 0 0
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Loop time of 0.0068838 on 4 procs for 1 steps with 360 atoms
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Pair time (%) = 0.000432014 (6.27581)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000115931 (1.68411)
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Outpt time (%) = 0.00171983 (24.9838)
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Other time (%) = 0.00461602 (67.0563)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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change_box all y scale 1.01 remap
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Changing box ...
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orthogonal box = (-6.12 -20.604 -6.12) to (6.12 20.604 6.12)
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fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
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ATC: created function : 0 + 0(x-0)+0.01(y-0)+0(z-0)
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run 1
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Setting up run ...
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Memory usage per processor = 41.8034 Mbytes
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Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
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4 -1414.1262 0.34311553 0.33071491 0.33071491 0 -19.5738 0.3 -19.5738 41.208 0.408 0.01
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5 -1414.1262 0.34311553 0.33071491 0.33071491 0.34908704 -19.5738 0.3 -19.5738 41.208 0.408 0.01
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Loop time of 0.00684071 on 4 procs for 1 steps with 360 atoms
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Pair time (%) = 0.000422955 (6.18291)
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Neigh time (%) = 0 (0)
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Comm time (%) = 8.39233e-05 (1.22682)
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Outpt time (%) = 0.00172395 (25.2013)
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Other time (%) = 0.00460988 (67.389)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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change_box all y scale 1.01 remap
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Changing box ...
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orthogonal box = (-6.12 -20.81 -6.12) to (6.12 20.81 6.12)
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fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
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ATC: created function : 0 + 0(x-0)+0.0201(y-0)+0(z-0)
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run 1
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Setting up run ...
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Memory usage per processor = 41.8034 Mbytes
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Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
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5 -1413.1082 1.3610604 0.33071491 0.33071491 0 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201
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6 -1413.1082 1.3610604 0.33071491 0.33071491 1.0612595 -19.769538 0.3 -19.769538 41.62008 0.82008 0.0201
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Loop time of 0.00686866 on 4 procs for 1 steps with 360 atoms
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Pair time (%) = 0.000416577 (6.06489)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.000141203 (2.05576)
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Outpt time (%) = 0.00175518 (25.5534)
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Other time (%) = 0.0045557 (66.3259)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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change_box all y scale 1.01 remap
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Changing box ...
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orthogonal box = (-6.12 -21.0181 -6.12) to (6.12 21.0181 6.12)
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fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
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ATC: created function : 0 + 0(x-0)+0.030301(y-0)+0(z-0)
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run 1
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Setting up run ...
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Memory usage per processor = 41.8034 Mbytes
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Step TotEng pe KinEng ATC[1] ATC[2] x v x2 Ly dL strain
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6 -1411.4328 3.0364818 0.33071491 0.33071491 0 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301
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7 -1411.4328 3.0364818 0.33071491 0.33071491 1.7947982 -19.967233 0.3 -19.967233 42.036281 1.2362808 0.030301
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Loop time of 0.00686812 on 4 procs for 1 steps with 360 atoms
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Pair time (%) = 0.000451982 (6.58087)
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Neigh time (%) = 0 (0)
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Comm time (%) = 6.69956e-05 (0.975457)
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Outpt time (%) = 0.00174725 (25.44)
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Other time (%) = 0.0046019 (67.0037)
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Nlocal: 90 ave 90 max 90 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1184 ave 1184 max 1184 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3870 ave 3870 max 3870 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 7740 ave 7740 max 7740 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 30960
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Ave neighs/atom = 86
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Neighbor list builds = 0
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Dangerous builds = 0
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