benchmark test on tersoff shift
This commit is contained in:
Wengen Ouyang
98
examples/USER/misc/tersoff_shift/after_change.lmp
Normal file
98
examples/USER/misc/tersoff_shift/after_change.lmp
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LAMMPS (30 Nov 2020)
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# Initialization
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units metal
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boundary p p p
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atom_style charge
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use different molecule ids for each layer of hBN
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# so that inter- and intra-layer
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# interactions can be specified separately
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read_data hBN-momolayer-5nm.data
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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880 atoms
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read_data CPU = 0.007 seconds
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mass 1 10.8110 # boron mass (g/mole) | membrane
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mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
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######################## Potential defition ########################
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pair_style tersoff shift 0.05
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pair_coeff * * BNC.tersoff B N
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Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
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####################################################################
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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#### Simulation settings ####
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timestep 0.001
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#velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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############# Output ###############
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thermo 100
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thermo_style custom step etotal pe ke temp
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thermo_modify lost warn
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###### Run molecular dynamics ######
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run 1000
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Neighbor list info ...
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update every 1 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 = 4.1
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ghost atom cutoff = 4.1
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binsize = 2.05, bins = 23 24 49
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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) = 3.670 | 3.670 | 3.670 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -6604.6119 -6604.6119 0 0
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100 -6604.6147 -6604.831 0.21628592 1.9035958
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200 -6604.6142 -6604.812 0.19784607 1.7413013
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300 -6604.6146 -6604.8412 0.22652026 1.9936713
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400 -6604.6143 -6604.7986 0.18429458 1.6220306
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500 -6604.614 -6604.7824 0.16835542 1.4817454
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600 -6604.6145 -6604.8173 0.20279935 1.7848965
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700 -6604.6148 -6604.8472 0.23241961 2.0455932
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800 -6604.6141 -6604.8086 0.19442247 1.7111692
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900 -6604.6146 -6604.8192 0.20463626 1.8010637
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1000 -6604.6139 -6604.7789 0.16495493 1.4518167
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Loop time of 2.01396 on 1 procs for 1000 steps with 880 atoms
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Performance: 42.901 ns/day, 0.559 hours/ns, 496.535 timesteps/s
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99.5% 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 | 1.9741 | 1.9741 | 1.9741 | 0.0 | 98.02
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.013615 | 0.013615 | 0.013615 | 0.0 | 0.68
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Output | 0.00099606 | 0.00099606 | 0.00099606 | 0.0 | 0.05
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Modify | 0.014839 | 0.014839 | 0.014839 | 0.0 | 0.74
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Other | | 0.01045 | | | 0.52
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Nlocal: 880.000 ave 880 max 880 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1518.00 ave 1518 max 1518 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: 15840.0 ave 15840 max 15840 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 15840
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Ave neighs/atom = 18.000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:02
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98
examples/USER/misc/tersoff_shift/before_change.lmp
Normal file
98
examples/USER/misc/tersoff_shift/before_change.lmp
Normal file
@ -0,0 +1,98 @@
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LAMMPS (30 Nov 2020)
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# Initialization
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units metal
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boundary p p p
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atom_style charge
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processors * * 1 # domain decomposition over x and y
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# System and atom definition
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# we use different molecule ids for each layer of hBN
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# so that inter- and intra-layer
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# interactions can be specified separately
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read_data hBN-momolayer-5nm.data
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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880 atoms
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read_data CPU = 0.014 seconds
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mass 1 10.8110 # boron mass (g/mole) | membrane
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mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
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######################## Potential defition ########################
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pair_style tersoff shift 0.05
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pair_coeff * * BNC.tersoff B N
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Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
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####################################################################
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# Neighbor update settings
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neighbor 2.0 bin
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neigh_modify every 1
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neigh_modify delay 0
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neigh_modify check yes
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#### Simulation settings ####
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timestep 0.001
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#velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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############# Output ###############
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thermo 100
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thermo_style custom step etotal pe ke temp
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thermo_modify lost warn
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###### Run molecular dynamics ######
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run 1000
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Neighbor list info ...
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update every 1 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 = 4.1
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ghost atom cutoff = 4.1
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binsize = 2.05, bins = 23 24 49
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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) = 3.670 | 3.670 | 3.670 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -6604.6119 -6604.6119 0 0
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100 -6604.6148 -6604.831 0.21618057 1.9026686
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200 -6604.6142 -6604.812 0.19780992 1.7409831
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300 -6604.6147 -6604.8411 0.22645852 1.9931278
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400 -6604.6143 -6604.7988 0.1844863 1.623718
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500 -6604.6141 -6604.7823 0.16817044 1.4801174
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600 -6604.6145 -6604.8172 0.20269951 1.7840178
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700 -6604.6149 -6604.8489 0.23401257 2.0596132
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800 -6604.6142 -6604.8089 0.19466676 1.7133192
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900 -6604.6146 -6604.8186 0.20395195 1.7950409
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1000 -6604.614 -6604.778 0.1640674 1.4440053
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Loop time of 1.62583 on 1 procs for 1000 steps with 880 atoms
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Performance: 53.142 ns/day, 0.452 hours/ns, 615.069 timesteps/s
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99.0% 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 | 1.5875 | 1.5875 | 1.5875 | 0.0 | 97.64
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.013392 | 0.013392 | 0.013392 | 0.0 | 0.82
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Output | 0.00091558 | 0.00091558 | 0.00091558 | 0.0 | 0.06
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Modify | 0.014704 | 0.014704 | 0.014704 | 0.0 | 0.90
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Other | | 0.009355 | | | 0.58
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Nlocal: 880.000 ave 880 max 880 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1518.00 ave 1518 max 1518 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: 15840.0 ave 15840 max 15840 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 15840
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Ave neighs/atom = 18.000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:01
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@ -13,7 +13,7 @@ mass 1 10.8110 # boron mass (g/mole) | membrane
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mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
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mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
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######################## Potential defition ########################
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######################## Potential defition ########################
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pair_style tersoff shift 0.0
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pair_style tersoff shift 0.05
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pair_coeff * * BNC.tersoff B N
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pair_coeff * * BNC.tersoff B N
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####################################################################
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####################################################################
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# Neighbor update settings
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# Neighbor update settings
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@ -24,7 +24,7 @@ neigh_modify check yes
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#### Simulation settings ####
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#### Simulation settings ####
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timestep 0.001
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timestep 0.001
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velocity all create 300.0 12345 loop geom
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#velocity all create 300.0 12345 loop geom
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fix thermostat all nve
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fix thermostat all nve
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############# Output ###############
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############# Output ###############
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