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Merge pull request #4087 from akohlmey/add-rebomos-pair-style

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Add rebomos pair style with examples and unit test
This commit is contained in:
Axel Kohlmeyer
2024-02-26 11:38:10 -05:00
committed by GitHub
parent 6c3c724f9c 01d9f78e69
commit 8501c3de6c
19 changed files with 2876 additions and 1 deletions
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1
examples/threebody/MoS.rebomos Symbolic link
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../../potentials/MoS.rebomos

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examples/threebody/in.mos2-bulk Normal file
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units metal
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 &
a2 -1.5964590311 2.7651481541 0.0000000000 &
a3 0.0000000000 0.0000000000 13.9827680588 &
basis 0.0000000000 0.000000000 $(3.0/4.0) &
basis 0.0000000000 0.000000000 $(1.0/4.0) &
basis $(2.0/3.0) $(1.0/3.0) 0.862008989 &
basis $(1.0/3.0) $(2.0/3.0) 0.137990996 &
basis $(1.0/3.0) $(2.0/3.0) 0.362008989 &
basis $(2.0/3.0) $(1.0/3.0) 0.637991011 &
origin 0.1 0.1 0.1
region box prism 0 4 0 8 0 1 -2.0 0.0 0.0
create_box 2 box
create_atoms 2 box &
basis 1 1 &
basis 2 1 &
basis 3 2 &
basis 4 2 &
basis 5 2 &
basis 6 2
mass 1 95.95 #Mo
mass 2 32.065 #S
pair_style rebomos
pair_coeff * * MoS.rebomos Mo S
thermo_style custom step temp press pe ke cellgamma vol
thermo 10
#dump 1 all atom 10 MoS.lammpstrj
fix 1 all nve
run 20

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examples/threebody/in.mos2.rebomos Normal file
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# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_modify map array
atom_style atomic
read_data single_layer_MoS2.data
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style rebomos
pair_coeff * * MoS.rebomos Mo S S
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000

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examples/threebody/log.22Feb24.mos2-bulk.g++.1 Normal file
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
units metal
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 $(3.0/4.0) basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 0.33333333333333331483 0.637991011 origin 0.1 0.1 0.1
Lattice spacing in x,y,z = 4.7867748 2.7651482 13.982768
region box prism 0 4 0 8 0 1 -2.0 0.0 0.0
create_box 2 box
Created triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 2 box basis 1 1 basis 2 1 basis 3 2 basis 4 2 basis 5 2 basis 6 2
Created 288 atoms
using lattice units in triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
create_atoms CPU = 0.000 seconds
mass 1 95.95 #Mo
mass 2 32.065 #S
pair_style rebomos
pair_coeff * * MoS.rebomos Mo S
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
thermo_style custom step temp press pe ke cellgamma vol
thermo 10
#dump 1 all atom 10 MoS.lammpstrj
fix 1 all nve
run 20
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 5 4 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.996 | 4.996 | 4.996 Mbytes
Step Temp Press PotEng KinEng CellGamma Volume
0 0 28799.53 -2061.6112 0 113.40187 5922.4926
10 80.776057 13540.088 -2064.6132 2.9966028 113.40187 5922.4926
20 146.17503 -20669.371 -2067.0428 5.4227518 113.40187 5922.4926
Loop time of 0.058071 on 1 procs for 20 steps with 288 atoms
Performance: 29.757 ns/day, 0.807 hours/ns, 344.406 timesteps/s, 99.189 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.057666 | 0.057666 | 0.057666 | 0.0 | 99.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00024654 | 0.00024654 | 0.00024654 | 0.0 | 0.42
Output | 2.3975e-05 | 2.3975e-05 | 2.3975e-05 | 0.0 | 0.04
Modify | 3.8394e-05 | 3.8394e-05 | 3.8394e-05 | 0.0 | 0.07
Other | | 9.596e-05 | | | 0.17
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4285 ave 4285 max 4285 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: 142848 ave 142848 max 142848 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 142848
Ave neighs/atom = 496
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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examples/threebody/log.22Feb24.mos2-bulk.g++.4 Normal file
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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
units metal
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 $(3.0/4.0) basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 $(1.0/4.0) basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis $(2.0/3.0) $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 $(1.0/3.0) 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis $(1.0/3.0) $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 $(2.0/3.0) 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis $(1.0/3.0) $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 $(2.0/3.0) 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis $(2.0/3.0) $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 $(1.0/3.0) 0.637991011 origin 0.1 0.1 0.1
lattice custom 1.0 a1 3.1903157234 0.0000000000 0.0000000000 a2 -1.5964590311 2.7651481541 0.0000000000 a3 0.0000000000 0.0000000000 13.9827680588 basis 0.0000000000 0.000000000 0.75 basis 0.0000000000 0.000000000 0.25 basis 0.66666666666666662966 0.33333333333333331483 0.862008989 basis 0.33333333333333331483 0.66666666666666662966 0.137990996 basis 0.33333333333333331483 0.66666666666666662966 0.362008989 basis 0.66666666666666662966 0.33333333333333331483 0.637991011 origin 0.1 0.1 0.1
Lattice spacing in x,y,z = 4.7867748 2.7651482 13.982768
region box prism 0 4 0 8 0 1 -2.0 0.0 0.0
create_box 2 box
Created triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
2 by 2 by 1 MPI processor grid
create_atoms 2 box basis 1 1 basis 2 1 basis 3 2 basis 4 2 basis 5 2 basis 6 2
Created 288 atoms
using lattice units in triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
create_atoms CPU = 0.000 seconds
mass 1 95.95 #Mo
mass 2 32.065 #S
pair_style rebomos
pair_coeff * * MoS.rebomos Mo S
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
thermo_style custom step temp press pe ke cellgamma vol
thermo 10
#dump 1 all atom 10 MoS.lammpstrj
fix 1 all nve
run 20
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 5 4 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.15 | 4.151 | 4.151 Mbytes
Step Temp Press PotEng KinEng CellGamma Volume
0 0 28799.53 -2061.6112 0 113.40187 5922.4926
10 80.776057 13540.088 -2064.6132 2.9966028 113.40187 5922.4926
20 146.17503 -20669.371 -2067.0428 5.4227518 113.40187 5922.4926
Loop time of 0.0219485 on 4 procs for 20 steps with 288 atoms
Performance: 78.730 ns/day, 0.305 hours/ns, 911.225 timesteps/s, 262.433 katom-step/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.018118 | 0.019372 | 0.020087 | 0.5 | 88.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0015635 | 0.0023195 | 0.0035967 | 1.6 | 10.57
Output | 2.5017e-05 | 4.6834e-05 | 0.00010543 | 0.0 | 0.21
Modify | 1.3954e-05 | 1.423e-05 | 1.4594e-05 | 0.0 | 0.06
Other | | 0.0001957 | | | 0.89
Nlocal: 72 ave 72 max 72 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2771.5 ave 2775 max 2768 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 35712 ave 35712 max 35712 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 142848
Ave neighs/atom = 496
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_modify map array
atom_style atomic
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:219)
1 by 1 by 1 MPI processor grid
reading atoms ...
768 atoms
read_data CPU = 0.002 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style rebomos
pair_coeff * * MoS.rebomos Mo S S
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 12 7 30
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes
Step TotEng PotEng KinEng Temp
0 -5466.9785 -5496.7212 29.742759 300
500 -5466.964 -5482.6985 15.734505 158.7059
1000 -5466.9615 -5480.9492 13.98763 141.08607
1500 -5466.964 -5482.6912 15.727258 158.63281
2000 -5466.9657 -5483.3606 16.394878 165.36675
2500 -5466.9624 -5481.6253 14.662948 147.89765
3000 -5466.9642 -5482.7515 15.7873 159.23842
3500 -5466.9654 -5483.3789 16.413502 165.5546
4000 -5466.9628 -5481.848 14.885236 150.13977
4500 -5466.9648 -5483.5045 16.539775 166.82825
5000 -5466.9649 -5483.4932 16.528298 166.71249
Loop time of 19.1009 on 1 procs for 5000 steps with 768 atoms
Performance: 22.617 ns/day, 1.061 hours/ns, 261.768 timesteps/s, 201.038 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.042 | 19.042 | 19.042 | 0.0 | 99.69
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.018451 | 0.018451 | 0.018451 | 0.0 | 0.10
Output | 0.00015575 | 0.00015575 | 0.00015575 | 0.0 | 0.00
Modify | 0.023931 | 0.023931 | 0.023931 | 0.0 | 0.13
Other | | 0.01658 | | | 0.09
Nlocal: 768 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1158 ave 1158 max 1158 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: 141824 ave 141824 max 141824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 141824
Ave neighs/atom = 184.66667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:19

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LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_modify map array
atom_style atomic
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:219)
2 by 2 by 1 MPI processor grid
reading atoms ...
768 atoms
read_data CPU = 0.002 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style rebomos
pair_coeff * * MoS.rebomos Mo S S
Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
#########################################################################
### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 loop geom
############################
# Output
thermo 500
thermo_style custom step etotal pe ke temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 5000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 12 7 30
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.045 | 4.045 | 4.045 Mbytes
Step TotEng PotEng KinEng Temp
0 -5466.9785 -5496.7212 29.742759 300
500 -5466.964 -5482.6985 15.734505 158.7059
1000 -5466.9615 -5480.9492 13.98763 141.08607
1500 -5466.964 -5482.6912 15.727258 158.63281
2000 -5466.9657 -5483.3606 16.394878 165.36675
2500 -5466.9624 -5481.6253 14.662948 147.89765
3000 -5466.9642 -5482.7515 15.7873 159.23842
3500 -5466.9654 -5483.3789 16.413502 165.5546
4000 -5466.9628 -5481.848 14.885236 150.13977
4500 -5466.9648 -5483.5045 16.539775 166.82825
5000 -5466.9649 -5483.4932 16.528298 166.71249
Loop time of 5.69326 on 4 procs for 5000 steps with 768 atoms
Performance: 75.879 ns/day, 0.316 hours/ns, 878.231 timesteps/s, 674.482 katom-step/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 | 5.2611 | 5.3666 | 5.4358 | 3.0 | 94.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.23476 | 0.30106 | 0.40642 | 12.8 | 5.29
Output | 0.00014996 | 0.0004478 | 0.0013353 | 0.0 | 0.01
Modify | 0.0068861 | 0.0069917 | 0.0072247 | 0.2 | 0.12
Other | | 0.01814 | | | 0.32
Nlocal: 192 ave 194 max 190 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 710 ave 712 max 708 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 35456 ave 35824 max 35088 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 141824
Ave neighs/atom = 184.66667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05