repeatable example
This commit is contained in:
@ -18,7 +18,7 @@ bond_coeff 1 C 10 10 10
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angle_style mesocnt
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angle_style mesocnt
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angle_coeff 1 buckling C 10 10 10
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angle_coeff 1 buckling C 10 10 10
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pair_style mesocnt 30 chain
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pair_style mesocnt 40 chain
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pair_coeff * * C_10_10.mesocnt 1
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pair_coeff * * C_10_10.mesocnt 1
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# output
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# output
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@ -1,118 +0,0 @@
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LAMMPS (3 Aug 2022)
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# initialisation
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units metal
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dimension 3
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boundary p p s
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atom_style full
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special_bonds lj 1 1 1
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neigh_modify every 5 delay 0 check yes
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newton on
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read_data data.film_mesocnt
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Reading data file ...
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orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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79596 atoms
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scanning bonds ...
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1 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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79200 bonds
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reading angles ...
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78804 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.012 seconds
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read_data CPU = 0.158 seconds
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# force field
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bond_style mesocnt
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bond_coeff 1 C 10 10 10
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angle_style mesocnt
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angle_coeff 1 buckling C 10 10 10
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pair_style mesocnt 30 chain
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pair_coeff * * C_10_10.mesocnt 1
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Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
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# output
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thermo 100
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compute epair all pe pair
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compute ebond all pe bond
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compute eangle all pe angle
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compute epair_atom all pe/atom pair
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compute ebond_atom all pe/atom bond
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compute eangle_atom all pe/atom angle
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fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
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thermo_style custom step time cpu temp etotal ke pe c_ebond c_eangle c_epair
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dump custom all custom 1000 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
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# simulation setup
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velocity all create 600.0 2022
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timestep 0.01
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fix nvt all nvt temp 300.0 300.0 1
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run 100
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Neighbor list info ...
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update: every = 5 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 32
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ghost atom cutoff = 32
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binsize = 16, bins = 313 313 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair mesocnt, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 58.03 | 58.03 | 58.03 Mbytes
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Step Time CPU Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
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0 0 0 600 1355.9473 6173.0767 -4817.1294 28.668731 21.29199 -4867.0901
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100 1 3.0380832 322.67058 1292.7084 3319.7837 -2027.0754 1107.8055 2092.5049 -5227.3858
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Loop time of 3.03811 on 1 procs for 100 steps with 79596 atoms
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Performance: 28.439 ns/day, 0.844 hours/ns, 32.915 timesteps/s
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99.2% CPU use with 1 MPI tasks x no 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 | 2.5683 | 2.5683 | 2.5683 | 0.0 | 84.53
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Bond | 0.2957 | 0.2957 | 0.2957 | 0.0 | 9.73
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Neigh | 0.057597 | 0.057597 | 0.057597 | 0.0 | 1.90
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Comm | 0.0020917 | 0.0020917 | 0.0020917 | 0.0 | 0.07
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Output | 0.00011104 | 0.00011104 | 0.00011104 | 0.0 | 0.00
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Modify | 0.10993 | 0.10993 | 0.10993 | 0.0 | 3.62
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Other | | 0.004415 | | | 0.15
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Nlocal: 79596 ave 79596 max 79596 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1935 ave 1935 max 1935 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 659576 ave 659576 max 659576 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 659576
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Ave neighs/atom = 8.2865471
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Ave special neighs/atom = 5.9402985
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:04
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@ -1,118 +0,0 @@
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LAMMPS (3 Aug 2022)
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# initialisation
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units metal
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dimension 3
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boundary p p s
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atom_style full
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special_bonds lj 1 1 1
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neigh_modify every 5 delay 0 check yes
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newton on
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read_data data.film_mesocnt
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Reading data file ...
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orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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79596 atoms
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scanning bonds ...
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1 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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79200 bonds
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reading angles ...
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78804 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.005 seconds
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read_data CPU = 0.154 seconds
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# force field
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bond_style mesocnt
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bond_coeff 1 C 10 10 10
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angle_style mesocnt
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angle_coeff 1 buckling C 10 10 10
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pair_style mesocnt 30 chain
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pair_coeff * * C_10_10.mesocnt 1
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Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
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# output
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thermo 100
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compute epair all pe pair
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compute ebond all pe bond
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compute eangle all pe angle
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compute epair_atom all pe/atom pair
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compute ebond_atom all pe/atom bond
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compute eangle_atom all pe/atom angle
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fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
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thermo_style custom step time cpu temp etotal ke pe c_ebond c_eangle c_epair
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dump custom all custom 1000 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
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# simulation setup
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velocity all create 600.0 2022
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timestep 0.01
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fix nvt all nvt temp 300.0 300.0 1
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run 100
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Neighbor list info ...
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update: every = 5 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 32
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ghost atom cutoff = 32
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binsize = 16, bins = 313 313 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair mesocnt, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 21.56 | 21.57 | 21.6 Mbytes
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Step Time CPU Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
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0 0 0 600 1355.9473 6173.0767 -4817.1294 28.668731 21.29199 -4867.0901
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100 1 0.92993546 322.71889 1293.8436 3320.2808 -2026.4371 1107.7962 2093.0006 -5227.234
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Loop time of 0.929957 on 4 procs for 100 steps with 79596 atoms
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Performance: 92.908 ns/day, 0.258 hours/ns, 107.532 timesteps/s
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98.0% CPU use with 4 MPI tasks x no 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 | 0.58144 | 0.67551 | 0.78613 | 9.0 | 72.64
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Bond | 0.072245 | 0.077166 | 0.085344 | 1.8 | 8.30
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Neigh | 0.016299 | 0.016303 | 0.016308 | 0.0 | 1.75
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Comm | 0.011498 | 0.13156 | 0.23472 | 22.2 | 14.15
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Output | 6.3584e-05 | 6.9594e-05 | 8.0167e-05 | 0.0 | 0.01
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Modify | 0.020663 | 0.026031 | 0.028517 | 1.9 | 2.80
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Other | | 0.003318 | | | 0.36
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Nlocal: 19899 ave 21952 max 18667 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 1000.75 ave 1070 max 947 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 164894 ave 187180 max 151353 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Total # of neighbors = 659576
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Ave neighs/atom = 8.2865471
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Ave special neighs/atom = 5.9402985
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:02
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126
examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1
Normal file
126
examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1
Normal file
@ -0,0 +1,126 @@
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LAMMPS (3 Aug 2022)
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# initialisation
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||||||
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|
||||||
|
units metal
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dimension 3
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||||||
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boundary p p s
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||||||
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atom_style full
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||||||
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special_bonds lj 1 1 1
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neigh_modify every 5 delay 0 check yes
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||||||
|
newton on
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||||||
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|
||||||
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read_data data.film_mesocnt
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||||||
|
Reading data file ...
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||||||
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orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
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||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
79596 atoms
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||||||
|
scanning bonds ...
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||||||
|
1 = max bonds/atom
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||||||
|
scanning angles ...
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||||||
|
1 = max angles/atom
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||||||
|
reading bonds ...
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||||||
|
79200 bonds
|
||||||
|
reading angles ...
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||||||
|
78804 angles
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
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||||||
|
special bond factors lj: 1 1 1
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||||||
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special bond factors coul: 0 0 0
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||||||
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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||||||
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6 = max # of special neighbors
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||||||
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special bonds CPU = 0.012 seconds
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||||||
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read_data CPU = 0.160 seconds
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|
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# force field
|
||||||
|
|
||||||
|
bond_style mesocnt
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||||||
|
bond_coeff 1 C 10 10 10
|
||||||
|
|
||||||
|
angle_style mesocnt
|
||||||
|
angle_coeff 1 buckling C 10 10 10
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||||||
|
|
||||||
|
pair_style mesocnt 40 chain
|
||||||
|
pair_coeff * * C_10_10.mesocnt 1
|
||||||
|
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
compute epair all pe pair
|
||||||
|
compute ebond all pe bond
|
||||||
|
compute eangle all pe angle
|
||||||
|
|
||||||
|
compute epair_atom all pe/atom pair
|
||||||
|
compute ebond_atom all pe/atom bond
|
||||||
|
compute eangle_atom all pe/atom angle
|
||||||
|
|
||||||
|
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair
|
||||||
|
thermo 10
|
||||||
|
#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
|
||||||
|
|
||||||
|
# simulation setup
|
||||||
|
|
||||||
|
velocity all create 600.0 2022 loop geom
|
||||||
|
timestep 0.01
|
||||||
|
fix nvt all nvt temp 300.0 300.0 1
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 5 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 42
|
||||||
|
ghost atom cutoff = 42
|
||||||
|
binsize = 21, bins = 239 239 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair mesocnt, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 49.89 | 49.89 | 49.89 Mbytes
|
||||||
|
Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
|
||||||
|
0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639
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||||||
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10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597
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||||||
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20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945
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30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586
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40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382
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50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005
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60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242
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70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807
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80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611
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90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41
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100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831
|
||||||
|
Loop time of 4.1637 on 1 procs for 100 steps with 79596 atoms
|
||||||
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|
||||||
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Performance: 20.751 ns/day, 1.157 hours/ns, 24.017 timesteps/s
|
||||||
|
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.705 | 3.705 | 3.705 | 0.0 | 88.98
|
||||||
|
Bond | 0.29317 | 0.29317 | 0.29317 | 0.0 | 7.04
|
||||||
|
Neigh | 0.078491 | 0.078491 | 0.078491 | 0.0 | 1.89
|
||||||
|
Comm | 0.0019462 | 0.0019462 | 0.0019462 | 0.0 | 0.05
|
||||||
|
Output | 0.00099817 | 0.00099817 | 0.00099817 | 0.0 | 0.02
|
||||||
|
Modify | 0.079874 | 0.079874 | 0.079874 | 0.0 | 1.92
|
||||||
|
Other | | 0.004224 | | | 0.10
|
||||||
|
|
||||||
|
Nlocal: 79596 ave 79596 max 79596 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2567 ave 2567 max 2567 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 1.1337e+06 ave 1.1337e+06 max 1.1337e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 1133696
|
||||||
|
Ave neighs/atom = 14.243128
|
||||||
|
Ave special neighs/atom = 5.9402985
|
||||||
|
Neighbor list builds = 2
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:05
|
||||||
126
examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4
Normal file
126
examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4
Normal file
@ -0,0 +1,126 @@
|
|||||||
|
LAMMPS (3 Aug 2022)
|
||||||
|
# initialisation
|
||||||
|
|
||||||
|
units metal
|
||||||
|
dimension 3
|
||||||
|
boundary p p s
|
||||||
|
atom_style full
|
||||||
|
special_bonds lj 1 1 1
|
||||||
|
neigh_modify every 5 delay 0 check yes
|
||||||
|
newton on
|
||||||
|
|
||||||
|
read_data data.film_mesocnt
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
79596 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
1 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
79200 bonds
|
||||||
|
reading angles ...
|
||||||
|
78804 angles
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 1 1 1
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.005 seconds
|
||||||
|
read_data CPU = 0.156 seconds
|
||||||
|
|
||||||
|
# force field
|
||||||
|
|
||||||
|
bond_style mesocnt
|
||||||
|
bond_coeff 1 C 10 10 10
|
||||||
|
|
||||||
|
angle_style mesocnt
|
||||||
|
angle_coeff 1 buckling C 10 10 10
|
||||||
|
|
||||||
|
pair_style mesocnt 40 chain
|
||||||
|
pair_coeff * * C_10_10.mesocnt 1
|
||||||
|
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
compute epair all pe pair
|
||||||
|
compute ebond all pe bond
|
||||||
|
compute eangle all pe angle
|
||||||
|
|
||||||
|
compute epair_atom all pe/atom pair
|
||||||
|
compute ebond_atom all pe/atom bond
|
||||||
|
compute eangle_atom all pe/atom angle
|
||||||
|
|
||||||
|
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
|
||||||
|
|
||||||
|
thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair
|
||||||
|
thermo 10
|
||||||
|
#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
|
||||||
|
|
||||||
|
# simulation setup
|
||||||
|
|
||||||
|
velocity all create 600.0 2022 loop geom
|
||||||
|
timestep 0.01
|
||||||
|
fix nvt all nvt temp 300.0 300.0 1
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 5 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 42
|
||||||
|
ghost atom cutoff = 42
|
||||||
|
binsize = 21, bins = 239 239 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair mesocnt, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 16.47 | 16.58 | 16.89 Mbytes
|
||||||
|
Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
|
||||||
|
0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639
|
||||||
|
10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597
|
||||||
|
20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945
|
||||||
|
30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586
|
||||||
|
40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382
|
||||||
|
50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005
|
||||||
|
60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242
|
||||||
|
70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807
|
||||||
|
80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611
|
||||||
|
90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41
|
||||||
|
100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831
|
||||||
|
Loop time of 1.25052 on 4 procs for 100 steps with 79596 atoms
|
||||||
|
|
||||||
|
Performance: 69.091 ns/day, 0.347 hours/ns, 79.967 timesteps/s
|
||||||
|
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.87036 | 0.97558 | 1.1135 | 9.0 | 78.01
|
||||||
|
Bond | 0.071751 | 0.076357 | 0.084244 | 1.7 | 6.11
|
||||||
|
Neigh | 0.023232 | 0.023239 | 0.023244 | 0.0 | 1.86
|
||||||
|
Comm | 0.0046002 | 0.15227 | 0.26319 | 24.1 | 12.18
|
||||||
|
Output | 0.00032696 | 0.00037811 | 0.00045537 | 0.0 | 0.03
|
||||||
|
Modify | 0.019263 | 0.020646 | 0.023155 | 1.1 | 1.65
|
||||||
|
Other | | 0.00204 | | | 0.16
|
||||||
|
|
||||||
|
Nlocal: 19899 ave 21951 max 18670 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 1323.5 ave 1412 max 1255 min
|
||||||
|
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 283424 ave 325466 max 258171 min
|
||||||
|
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1133696
|
||||||
|
Ave neighs/atom = 14.243128
|
||||||
|
Ave special neighs/atom = 5.9402985
|
||||||
|
Neighbor list builds = 2
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
Reference in New Issue
Block a user