mirror of https://github.com/lammps/lammps.git
Created new set of tests for Tersoff variants
This commit is contained in:
Aidan Thompson
parent
b28f6cb8ca
commit
7bff94910f
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@ -112,7 +112,8 @@ steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
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streitz: Streitz-Mintmire potential for Al2O3
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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template: examples for using atom_style template and comparing to atom style molecular
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threebody: regression test input for a variety of manybody potentials
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tersoff: regression test input for Tersoff variants
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threebody: regression test input for a variety of threebody potentials
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vashishta: models using the Vashishta potential
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voronoi: Voronoi tesselation via compute voronoi/atom command
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wall: use of reflective walls with different stochastic models
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@ -0,0 +1 @@
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../../potentials/BNC.tersoff
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@ -0,0 +1 @@
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../../potentials/Si.tersoff
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@ -0,0 +1,135 @@
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# Simple regression tests for Tersoff potentials
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# NOTE: These are not intended to represent real materials
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# cubic diamond unit cell
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variable a equal 5.431
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lattice custom $a &
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a1 1.0 0.0 0.0 &
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a2 0.0 1.0 0.0 &
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a3 0.0 0.0 1.0 &
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basis 0.0 0.0 0.0 &
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basis 0.0 0.5 0.5 &
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basis 0.5 0.0 0.5 &
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basis 0.5 0.5 0.0 &
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basis 0.25 0.25 0.25 &
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basis 0.25 0.75 0.75 &
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basis 0.75 0.25 0.75 &
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basis 0.75 0.75 0.25
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region myreg block 0 4 &
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0 4 &
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0 4
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create_box 8 myreg
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create_atoms 1 region myreg &
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basis 1 1 &
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basis 2 2 &
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basis 3 3 &
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basis 4 4 &
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basis 5 5 &
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basis 6 6 &
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basis 7 7 &
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basis 8 8
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mass * 28.06
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velocity all create $t 5287287 loop geom
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# Equilibrate using Tersoff model for silicon
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pair_style tersoff
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pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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write_restart restart.equil
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# Test Tersoff/Mod model for Si
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clear
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read_restart restart.equil
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pair_style tersoff/mod
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pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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# Test Tersoff/Mod/C model for Si
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clear
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read_restart restart.equil
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newton on on
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pair_style tersoff/mod/c
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pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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# Test Tersoff model for B/N/C
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clear
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read_restart restart.equil
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variable fac equal 0.6
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change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
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pair_style tersoff
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pair_coeff * * BNC.tersoff N N N C B B C B
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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# Test Tersoff model for B/N/C
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clear
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read_restart restart.equil
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variable fac equal 0.6
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change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
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pair_style tersoff shift 0.05
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pair_coeff * * BNC.tersoff N N N C B B C B
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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@ -0,0 +1,472 @@
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LAMMPS (24 Dec 2020)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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using 1 OpenMP thread(s) per MPI task
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# Simple regression tests for Tersoff potentials
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# NOTE: These are not intended to represent real materials
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# cubic diamond unit cell
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variable a equal 5.431
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lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
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region myreg block 0 4 0 4 0 4
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create_box 8 myreg
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
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Created 512 atoms
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create_atoms CPU = 0.000 seconds
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mass * 28.06
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velocity all create $t 5287287 loop geom
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velocity all create 1800 5287287 loop geom
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# Equilibrate using Tersoff model for silicon
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pair_style tersoff
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pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
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Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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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 = 4.2
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ghost atom cutoff = 4.2
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binsize = 2.1, bins = 11 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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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) = 2.985 | 2.985 | 2.985 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1800 -2370.771 0 -2251.8775 12511.419
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10 1144.7447 -2327.3227 0 -2251.7759 21852.599
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20 770.19243 -2302.1547 0 -2251.7633 22286.587
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30 1059.4324 -2320.1988 0 -2251.8159 6242.222
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40 1000.972 -2314.6531 0 -2251.796 -3069.9273
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50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
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60 761.38639 -2296.1731 0 -2251.7928 -14520.921
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70 750.57677 -2294.3086 0 -2251.7965 -21400.198
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80 676.66672 -2288.2634 0 -2251.7899 -23480.201
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90 640.24103 -2284.6678 0 -2251.7848 -20659.983
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100 742.67188 -2290.0616 0 -2251.7855 -16211.799
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Loop time of 0.107338 on 1 procs for 100 steps with 512 atoms
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Performance: 80.493 ns/day, 0.298 hours/ns, 931.637 timesteps/s
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98.6% 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 | 0.10455 | 0.10455 | 0.10455 | 0.0 | 97.40
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Neigh | 0.001115 | 0.001115 | 0.001115 | 0.0 | 1.04
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Comm | 0.000482 | 0.000482 | 0.000482 | 0.0 | 0.45
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Output | 0.000194 | 0.000194 | 0.000194 | 0.0 | 0.18
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Modify | 0.000787 | 0.000787 | 0.000787 | 0.0 | 0.73
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Other | | 0.000209 | | | 0.19
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Nlocal: 512.000 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 857.000 ave 857 max 857 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 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: 8404.00 ave 8404 max 8404 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 8404
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Ave neighs/atom = 16.414062
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Neighbor list builds = 2
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Dangerous builds = 0
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write_restart restart.equil
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System init for write_restart ...
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# Test Tersoff/Mod model for Si
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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pair style tersoff stores no restart info
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512 atoms
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read_restart CPU = 0.006 seconds
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pair_style tersoff/mod
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pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
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Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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All restart file global fix info was re-assigned
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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 = 4.3
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ghost atom cutoff = 4.3
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binsize = 2.15, bins = 11 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff/mod, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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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) = 2.979 | 2.979 | 2.979 Mbytes
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Step Temp E_pair E_mol TotEng Press
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100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
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110 1135.5853 -2234.6974 0 -2172.3908 113.80404
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120 1462.8415 -2253.8186 0 -2172.3853 10922.229
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130 1755.9617 -2270.5152 0 -2172.3964 18780.707
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140 1895.1939 -2277.1484 0 -2172.3965 22357.106
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150 1869.5375 -2273.2734 0 -2172.3851 22616.492
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160 1824.0448 -2268.4342 0 -2172.393 19254.299
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170 1637.9038 -2254.5219 0 -2172.3815 15904.928
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180 1451.9871 -2240.7199 0 -2172.3771 12064.754
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190 1362.8248 -2233.1942 0 -2172.3789 7970.534
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200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
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Loop time of 0.128972 on 1 procs for 100 steps with 512 atoms
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Performance: 66.991 ns/day, 0.358 hours/ns, 775.362 timesteps/s
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98.6% 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 | 0.12498 | 0.12498 | 0.12498 | 0.0 | 96.91
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Neigh | 0.002322 | 0.002322 | 0.002322 | 0.0 | 1.80
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Comm | 0.000537 | 0.000537 | 0.000537 | 0.0 | 0.42
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Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.14
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Modify | 0.000761 | 0.000761 | 0.000761 | 0.0 | 0.59
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Other | | 0.000192 | | | 0.15
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Nlocal: 512.000 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 960.000 ave 960 max 960 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 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: 9244.00 ave 9244 max 9244 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9244
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Ave neighs/atom = 18.054688
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Neighbor list builds = 4
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Dangerous builds = 0
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# Test Tersoff/Mod/C model for Si
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
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restoring atom style atomic from restart
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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pair style tersoff stores no restart info
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512 atoms
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read_restart CPU = 0.001 seconds
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newton on on
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pair_style tersoff/mod/c
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pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
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Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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fix_modify 1 energy yes
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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All restart file global fix info was re-assigned
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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 = 4.205694
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ghost atom cutoff = 4.205694
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binsize = 2.102847, bins = 11 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff/mod/c, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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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) = 2.976 | 2.976 | 2.976 Mbytes
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Step Temp E_pair E_mol TotEng Press
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100 742.67188 -2221.9308 0 -2183.6547 -11721.269
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110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
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120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
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130 1487.0219 -2264.3656 0 -2183.6707 14660.783
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140 1709.1746 -2276.4761 0 -2183.6886 19298.791
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150 1710.6528 -2274.1129 0 -2183.6764 22026.559
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160 1651.0659 -2267.9877 0 -2183.6699 20916.722
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170 1632.7705 -2264.7081 0 -2183.6777 17339.031
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180 1477.693 -2252.4683 0 -2183.6706 12563.594
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190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
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200 1356.7172 -2240.5315 0 -2183.668 5584.6734
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Loop time of 0.133106 on 1 procs for 100 steps with 512 atoms
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Performance: 64.911 ns/day, 0.370 hours/ns, 751.281 timesteps/s
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96.0% 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 | 0.1291 | 0.1291 | 0.1291 | 0.0 | 96.99
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Neigh | 0.002343 | 0.002343 | 0.002343 | 0.0 | 1.76
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Comm | 0.0005 | 0.0005 | 0.0005 | 0.0 | 0.38
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Output | 0.000186 | 0.000186 | 0.000186 | 0.0 | 0.14
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Modify | 0.000786 | 0.000786 | 0.000786 | 0.0 | 0.59
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Other | | 0.000191 | | | 0.14
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||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 903.000 ave 903 max 903 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 8414.00 ave 8414 max 8414 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8414
|
||||
Ave neighs/atom = 16.433594
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 0 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
|
||||
Loop time of 0.134621 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 64.180 ns/day, 0.374 hours/ns, 742.826 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.12837 | 0.12837 | 0.12837 | 0.0 | 95.35
|
||||
Neigh | 0.004553 | 0.004553 | 0.004553 | 0.0 | 3.38
|
||||
Comm | 0.000601 | 0.000601 | 0.000601 | 0.0 | 0.45
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.13
|
||||
Modify | 0.000742 | 0.000742 | 0.000742 | 0.0 | 0.55
|
||||
Other | | 0.000181 | | | 0.13
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1051.00 ave 1051 max 1051 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14760.0 ave 14760 max 14760 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14760
|
||||
Ave neighs/atom = 28.828125
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 0 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 0 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
|
||||
Loop time of 0.120764 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 71.545 ns/day, 0.335 hours/ns, 828.061 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11521 | 0.11521 | 0.11521 | 0.0 | 95.40
|
||||
Neigh | 0.003874 | 0.003874 | 0.003874 | 0.0 | 3.21
|
||||
Comm | 0.000542 | 0.000542 | 0.000542 | 0.0 | 0.45
|
||||
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.15
|
||||
Modify | 0.000774 | 0.000774 | 0.000774 | 0.0 | 0.64
|
||||
Other | | 0.00019 | | | 0.16
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1037.00 ave 1037 max 1037 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14676.0 ave 14676 max 14676 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14676
|
||||
Ave neighs/atom = 28.664062
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,472 @@
|
|||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple regression tests for Tersoff potentials
|
||||
|
||||
# NOTE: These are not intended to represent real materials
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# cubic diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
|
||||
create_box 8 myreg
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass * 28.06
|
||||
|
||||
velocity all create $t 5287287 loop geom
|
||||
velocity all create 1800 5287287 loop geom
|
||||
|
||||
# Equilibrate using Tersoff model for silicon
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
|
||||
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.2
|
||||
ghost atom cutoff = 4.2
|
||||
binsize = 2.1, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1800 -2370.771 0 -2251.8775 12511.419
|
||||
10 1144.7447 -2327.3227 0 -2251.7759 21852.599
|
||||
20 770.19243 -2302.1547 0 -2251.7633 22286.587
|
||||
30 1059.4324 -2320.1988 0 -2251.8159 6242.222
|
||||
40 1000.972 -2314.6531 0 -2251.796 -3069.9273
|
||||
50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
|
||||
60 761.38639 -2296.1731 0 -2251.7928 -14520.921
|
||||
70 750.57677 -2294.3086 0 -2251.7965 -21400.198
|
||||
80 676.66672 -2288.2634 0 -2251.7899 -23480.201
|
||||
90 640.24103 -2284.6678 0 -2251.7848 -20659.983
|
||||
100 742.67188 -2290.0616 0 -2251.7855 -16211.799
|
||||
Loop time of 0.0321762 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 268.521 ns/day, 0.089 hours/ns, 3107.882 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.026599 | 0.02712 | 0.027602 | 0.2 | 84.28
|
||||
Neigh | 0.000285 | 0.00028875 | 0.000294 | 0.0 | 0.90
|
||||
Comm | 0.003471 | 0.0039375 | 0.004446 | 0.6 | 12.24
|
||||
Output | 0.000112 | 0.00013675 | 0.000203 | 0.0 | 0.43
|
||||
Modify | 0.000443 | 0.0004555 | 0.000471 | 0.0 | 1.42
|
||||
Other | | 0.000238 | | | 0.74
|
||||
|
||||
Nlocal: 128.000 ave 131 max 126 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 447.750 ave 453 max 440 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2101.00 ave 2152 max 2032 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 8404
|
||||
Ave neighs/atom = 16.414062
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
write_restart restart.equil
|
||||
System init for write_restart ...
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.002 seconds
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.950 | 2.950 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
|
||||
110 1135.5853 -2234.6974 0 -2172.3908 113.80404
|
||||
120 1462.8415 -2253.8186 0 -2172.3853 10922.229
|
||||
130 1755.9617 -2270.5152 0 -2172.3964 18780.707
|
||||
140 1895.1939 -2277.1484 0 -2172.3965 22357.106
|
||||
150 1869.5375 -2273.2734 0 -2172.3851 22616.492
|
||||
160 1824.0448 -2268.4342 0 -2172.393 19254.299
|
||||
170 1637.9038 -2254.5219 0 -2172.3815 15904.928
|
||||
180 1451.9871 -2240.7199 0 -2172.3771 12064.754
|
||||
190 1362.8248 -2233.1942 0 -2172.3789 7970.534
|
||||
200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
|
||||
Loop time of 0.0389003 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 222.107 ns/day, 0.108 hours/ns, 2570.678 timesteps/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.031362 | 0.032656 | 0.033605 | 0.5 | 83.95
|
||||
Neigh | 0.000575 | 0.000599 | 0.000613 | 0.0 | 1.54
|
||||
Comm | 0.003768 | 0.004733 | 0.006014 | 1.2 | 12.17
|
||||
Output | 0.000207 | 0.00022525 | 0.000276 | 0.0 | 0.58
|
||||
Modify | 0.000445 | 0.00047975 | 0.0005 | 0.0 | 1.23
|
||||
Other | | 0.0002077 | | | 0.53
|
||||
|
||||
Nlocal: 128.000 ave 135 max 123 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 491.500 ave 499 max 486 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2311.00 ave 2457 max 2192 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9244
|
||||
Ave neighs/atom = 18.054688
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
newton on on
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
|
||||
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.205694
|
||||
ghost atom cutoff = 4.205694
|
||||
binsize = 2.102847, bins = 11 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff/mod/c, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.949 | 2.949 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2221.9308 0 -2183.6547 -11721.269
|
||||
110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
|
||||
120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
|
||||
130 1487.0219 -2264.3656 0 -2183.6707 14660.783
|
||||
140 1709.1746 -2276.4761 0 -2183.6886 19298.791
|
||||
150 1710.6528 -2274.1129 0 -2183.6764 22026.559
|
||||
160 1651.0659 -2267.9877 0 -2183.6699 20916.722
|
||||
170 1632.7705 -2264.7081 0 -2183.6777 17339.031
|
||||
180 1477.693 -2252.4683 0 -2183.6706 12563.594
|
||||
190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
|
||||
200 1356.7172 -2240.5315 0 -2183.668 5584.6734
|
||||
Loop time of 0.039244 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 220.161 ns/day, 0.109 hours/ns, 2548.160 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.03126 | 0.032782 | 0.033915 | 0.5 | 83.53
|
||||
Neigh | 0.000599 | 0.000707 | 0.000821 | 0.0 | 1.80
|
||||
Comm | 0.00363 | 0.004893 | 0.006493 | 1.5 | 12.47
|
||||
Output | 0.000122 | 0.0001425 | 0.000192 | 0.0 | 0.36
|
||||
Modify | 0.000497 | 0.00050925 | 0.000522 | 0.0 | 1.30
|
||||
Other | | 0.0002105 | | | 0.54
|
||||
|
||||
Nlocal: 128.000 ave 133 max 124 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Nghost: 459.000 ave 470 max 452 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 2103.50 ave 2204 max 2014 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 8414
|
||||
Ave neighs/atom = 16.433594
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
|
||||
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
|
||||
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
|
||||
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
|
||||
140 3222.7773 -3141.7275 0 -2925.5369 2161607
|
||||
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
|
||||
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
|
||||
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
|
||||
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
|
||||
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
|
||||
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
|
||||
Loop time of 0.0488862 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 176.737 ns/day, 0.136 hours/ns, 2045.565 timesteps/s
|
||||
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.037364 | 0.039346 | 0.041066 | 0.8 | 80.49
|
||||
Neigh | 0.001207 | 0.0012568 | 0.00136 | 0.2 | 2.57
|
||||
Comm | 0.005218 | 0.007064 | 0.009117 | 1.9 | 14.45
|
||||
Output | 0.000173 | 0.00020325 | 0.000277 | 0.0 | 0.42
|
||||
Modify | 0.000709 | 0.000715 | 0.000723 | 0.0 | 1.46
|
||||
Other | | 0.0003008 | | | 0.62
|
||||
|
||||
Nlocal: 128.000 ave 132 max 123 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 543.000 ave 548 max 535 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3690.00 ave 3811 max 3529 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 14760
|
||||
Ave neighs/atom = 28.828125
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
|
||||
# Test Tersoff model for B/N/C
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
read_restart restart.equil
|
||||
Reading restart file ...
|
||||
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
|
||||
restoring atom style atomic from restart
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
pair style tersoff stores no restart info
|
||||
512 atoms
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
variable fac equal 0.6
|
||||
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
|
||||
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
||||
Changing box ...
|
||||
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
|
||||
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
|
||||
|
||||
pair_style tersoff shift 0.05
|
||||
pair_coeff * * BNC.tersoff N N N C B B C B
|
||||
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
||||
|
||||
thermo 10
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
fix_modify 1 energy yes
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.1
|
||||
ghost atom cutoff = 3.1
|
||||
binsize = 1.55, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
|
||||
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
|
||||
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
|
||||
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
|
||||
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
|
||||
150 2215.3423 -3390.1427 0 -3255.8733 1138540
|
||||
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
|
||||
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
|
||||
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
|
||||
190 2339.5966 -3413.3961 0 -3254.7496 1088059
|
||||
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
|
||||
Loop time of 0.0409132 on 4 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 211.179 ns/day, 0.114 hours/ns, 2444.196 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.03285 | 0.033327 | 0.03406 | 0.3 | 81.46
|
||||
Neigh | 0.000975 | 0.0010677 | 0.001184 | 0.2 | 2.61
|
||||
Comm | 0.004915 | 0.005528 | 0.006044 | 0.7 | 13.51
|
||||
Output | 0.000129 | 0.0001535 | 0.000226 | 0.0 | 0.38
|
||||
Modify | 0.000564 | 0.0005885 | 0.000604 | 0.0 | 1.44
|
||||
Other | | 0.0002483 | | | 0.61
|
||||
|
||||
Nlocal: 128.000 ave 133 max 123 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 535.250 ave 542 max 531 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3669.00 ave 3822 max 3522 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 14676
|
||||
Ave neighs/atom = 28.664062
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
Loading…
Reference in New Issue