96 lines
3.9 KiB
Groff
96 lines
3.9 KiB
Groff
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
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using 1 OpenMP thread(s) per MPI task
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# monolayer MoS2
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units metal
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boundary p p f
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processors * * 1
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atom_modify map array
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atom_style atomic
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read_data single_layer_MoS2.data
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Reading data file ...
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triclinic box = (0 0 -100) to (51.15232 44.299209 100) with tilt (25.57616 0 0)
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WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:219)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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768 atoms
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read_data CPU = 0.002 seconds
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mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
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mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
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########################## Define potentials ################################
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pair_style rebomos
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pair_coeff * * MoS.rebomos Mo S S
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Reading rebomos potential file MoS.rebomos with DATE: 2013-11-04
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#########################################################################
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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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############################
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# Output
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thermo 500
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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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fix thermostat all nve
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run 5000
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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 = 13.4
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ghost atom cutoff = 13.4
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binsize = 6.7, bins = 12 7 30
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair rebomos, perpetual
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attributes: full, newton on, ghost
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.045 | 4.045 | 4.045 Mbytes
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Step TotEng PotEng KinEng Temp
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0 -5466.9785 -5496.7212 29.742759 300
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500 -5466.964 -5482.6985 15.734505 158.7059
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1000 -5466.9615 -5480.9492 13.98763 141.08607
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1500 -5466.964 -5482.6912 15.727258 158.63281
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2000 -5466.9657 -5483.3606 16.394878 165.36675
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2500 -5466.9624 -5481.6253 14.662948 147.89765
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3000 -5466.9642 -5482.7515 15.7873 159.23842
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3500 -5466.9654 -5483.3789 16.413502 165.5546
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4000 -5466.9628 -5481.848 14.885236 150.13977
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4500 -5466.9648 -5483.5045 16.539775 166.82825
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5000 -5466.9649 -5483.4932 16.528298 166.71249
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Loop time of 5.69326 on 4 procs for 5000 steps with 768 atoms
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Performance: 75.879 ns/day, 0.316 hours/ns, 878.231 timesteps/s, 674.482 katom-step/s
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98.6% CPU use with 4 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 | 5.2611 | 5.3666 | 5.4358 | 3.0 | 94.26
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.23476 | 0.30106 | 0.40642 | 12.8 | 5.29
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Output | 0.00014996 | 0.0004478 | 0.0013353 | 0.0 | 0.01
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Modify | 0.0068861 | 0.0069917 | 0.0072247 | 0.2 | 0.12
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Other | | 0.01814 | | | 0.32
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Nlocal: 192 ave 194 max 190 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Nghost: 710 ave 712 max 708 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 35456 ave 35824 max 35088 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Total # of neighbors = 141824
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Ave neighs/atom = 184.66667
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:05
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