From af993c95185d28130ef033f89e7e2ac451160d0c Mon Sep 17 00:00:00 2001 From: Wengen Ouyang Date: Tue, 5 Jan 2021 11:53:44 +0200 Subject: [PATCH] benchmark test on tersoff shift --- .../USER/misc/tersoff_shift/after_change.lmp | 98 +++++++++++++++++++ .../USER/misc/tersoff_shift/before_change.lmp | 98 +++++++++++++++++++ examples/USER/misc/tersoff_shift/in.hBN_shift | 4 +- 3 files changed, 198 insertions(+), 2 deletions(-) create mode 100644 examples/USER/misc/tersoff_shift/after_change.lmp create mode 100644 examples/USER/misc/tersoff_shift/before_change.lmp diff --git a/examples/USER/misc/tersoff_shift/after_change.lmp b/examples/USER/misc/tersoff_shift/after_change.lmp new file mode 100644 index 0000000000..f4644a7780 --- /dev/null +++ b/examples/USER/misc/tersoff_shift/after_change.lmp @@ -0,0 +1,98 @@ +LAMMPS (30 Nov 2020) +# Initialization +units metal +boundary p p p +atom_style charge +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately +read_data hBN-momolayer-5nm.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 880 atoms + read_data CPU = 0.007 seconds +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate + +######################## Potential defition ######################## +pair_style tersoff shift 0.05 +pair_coeff * * BNC.tersoff B N +Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +#velocity all create 300.0 12345 loop geom +fix thermostat all nve + +############# Output ############### +thermo 100 +thermo_style custom step etotal pe ke temp +thermo_modify lost warn + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 23 24 49 + 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) = 3.670 | 3.670 | 3.670 Mbytes +Step TotEng PotEng KinEng Temp + 0 -6604.6119 -6604.6119 0 0 + 100 -6604.6147 -6604.831 0.21628592 1.9035958 + 200 -6604.6142 -6604.812 0.19784607 1.7413013 + 300 -6604.6146 -6604.8412 0.22652026 1.9936713 + 400 -6604.6143 -6604.7986 0.18429458 1.6220306 + 500 -6604.614 -6604.7824 0.16835542 1.4817454 + 600 -6604.6145 -6604.8173 0.20279935 1.7848965 + 700 -6604.6148 -6604.8472 0.23241961 2.0455932 + 800 -6604.6141 -6604.8086 0.19442247 1.7111692 + 900 -6604.6146 -6604.8192 0.20463626 1.8010637 + 1000 -6604.6139 -6604.7789 0.16495493 1.4518167 +Loop time of 2.01396 on 1 procs for 1000 steps with 880 atoms + +Performance: 42.901 ns/day, 0.559 hours/ns, 496.535 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 | 1.9741 | 1.9741 | 1.9741 | 0.0 | 98.02 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013615 | 0.013615 | 0.013615 | 0.0 | 0.68 +Output | 0.00099606 | 0.00099606 | 0.00099606 | 0.0 | 0.05 +Modify | 0.014839 | 0.014839 | 0.014839 | 0.0 | 0.74 +Other | | 0.01045 | | | 0.52 + +Nlocal: 880.000 ave 880 max 880 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1518.00 ave 1518 max 1518 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: 15840.0 ave 15840 max 15840 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15840 +Ave neighs/atom = 18.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/tersoff_shift/before_change.lmp b/examples/USER/misc/tersoff_shift/before_change.lmp new file mode 100644 index 0000000000..2539ebd6a9 --- /dev/null +++ b/examples/USER/misc/tersoff_shift/before_change.lmp @@ -0,0 +1,98 @@ +LAMMPS (30 Nov 2020) +# Initialization +units metal +boundary p p p +atom_style charge +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately +read_data hBN-momolayer-5nm.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 880 atoms + read_data CPU = 0.014 seconds +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate + +######################## Potential defition ######################## +pair_style tersoff shift 0.05 +pair_coeff * * BNC.tersoff B N +Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +#velocity all create 300.0 12345 loop geom +fix thermostat all nve + +############# Output ############### +thermo 100 +thermo_style custom step etotal pe ke temp +thermo_modify lost warn + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 23 24 49 + 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) = 3.670 | 3.670 | 3.670 Mbytes +Step TotEng PotEng KinEng Temp + 0 -6604.6119 -6604.6119 0 0 + 100 -6604.6148 -6604.831 0.21618057 1.9026686 + 200 -6604.6142 -6604.812 0.19780992 1.7409831 + 300 -6604.6147 -6604.8411 0.22645852 1.9931278 + 400 -6604.6143 -6604.7988 0.1844863 1.623718 + 500 -6604.6141 -6604.7823 0.16817044 1.4801174 + 600 -6604.6145 -6604.8172 0.20269951 1.7840178 + 700 -6604.6149 -6604.8489 0.23401257 2.0596132 + 800 -6604.6142 -6604.8089 0.19466676 1.7133192 + 900 -6604.6146 -6604.8186 0.20395195 1.7950409 + 1000 -6604.614 -6604.778 0.1640674 1.4440053 +Loop time of 1.62583 on 1 procs for 1000 steps with 880 atoms + +Performance: 53.142 ns/day, 0.452 hours/ns, 615.069 timesteps/s +99.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5875 | 1.5875 | 1.5875 | 0.0 | 97.64 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013392 | 0.013392 | 0.013392 | 0.0 | 0.82 +Output | 0.00091558 | 0.00091558 | 0.00091558 | 0.0 | 0.06 +Modify | 0.014704 | 0.014704 | 0.014704 | 0.0 | 0.90 +Other | | 0.009355 | | | 0.58 + +Nlocal: 880.000 ave 880 max 880 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1518.00 ave 1518 max 1518 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: 15840.0 ave 15840 max 15840 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15840 +Ave neighs/atom = 18.000000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/misc/tersoff_shift/in.hBN_shift b/examples/USER/misc/tersoff_shift/in.hBN_shift index 3f05a405e2..e5afa45468 100644 --- a/examples/USER/misc/tersoff_shift/in.hBN_shift +++ b/examples/USER/misc/tersoff_shift/in.hBN_shift @@ -13,7 +13,7 @@ mass 1 10.8110 # boron mass (g/mole) | membrane mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate ######################## Potential defition ######################## -pair_style tersoff shift 0.0 +pair_style tersoff shift 0.05 pair_coeff * * BNC.tersoff B N #################################################################### # Neighbor update settings @@ -24,7 +24,7 @@ neigh_modify check yes #### Simulation settings #### timestep 0.001 -velocity all create 300.0 12345 loop geom +#velocity all create 300.0 12345 loop geom fix thermostat all nve ############# Output ###############