140 lines
6.6 KiB
Groff
140 lines
6.6 KiB
Groff
LAMMPS (5 Jun 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
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using 1 OpenMP thread(s) per MPI task
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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 full
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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 2 atom types so that inter- and intra-layer
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# interactions can be specified separately
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# read lammps data file
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read_data Bi_gr_AB_stack_2L_noH_300K.data
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orthogonal box = (0 0 0) to (42.6 41.8117 100)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1360 atoms
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reading velocities ...
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1360 velocities
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000187874 secs
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read_data CPU = 0.00234103 secs
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mass 1 12.0107 # carbon mass (g/mole) | membrane
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mass 2 12.0107 # carbon mass (g/mole) | adsorbate
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# Separate atom groups
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group membrane type 1
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680 atoms in group membrane
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group adsorbate type 2
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680 atoms in group adsorbate
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
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####################################################################
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pair_coeff * * rebo CH.rebo NULL C # chemical
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Reading potential file CH.rebo with DATE: 2018-7-3
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pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
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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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# calculate the COM
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variable adsxcom equal xcm(adsorbate,x)
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variable adsycom equal xcm(adsorbate,y)
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variable adszcom equal xcm(adsorbate,z)
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variable adsvxcom equal vcm(adsorbate,x)
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variable adsvycom equal vcm(adsorbate,y)
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variable adsvzcom equal vcm(adsorbate,z)
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#### Simulation settings ####
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timestep 0.001
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fix subf membrane setforce 0.0 0.0 0.0
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fix thermostat all nve
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compute 0 all pair rebo
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compute 1 all pair kolmogorov/crespi/full
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variable REBO equal c_0
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variable KC equal c_1
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############################
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# Output
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thermo 100
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thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
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thermo_modify line one format float %.10f
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thermo_modify flush yes norm no lost warn #ignore
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#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
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#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
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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 = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 5 5 12
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair rebo, perpetual, skip from (2)
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attributes: full, newton on, ghost
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pair build: skip/ghost
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stencil: none
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bin: none
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(2) pair kolmogorov/crespi/full, 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) = 11.13 | 11.13 | 11.13 Mbytes
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Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
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0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
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100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
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200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
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300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
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400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393291 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
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500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
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600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
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700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
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800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
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900 -5025.3984547938 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
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1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
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Loop time of 33.7338 on 4 procs for 1000 steps with 1360 atoms
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Performance: 2.561 ns/day, 9.370 hours/ns, 29.644 timesteps/s
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94.1% 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 | 30.833 | 31.356 | 32.18 | 9.1 | 92.95
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Bond | 0.00026059 | 0.00029182 | 0.00031185 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.443 | 2.2722 | 2.8091 | 34.3 | 6.74
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Output | 0.00068855 | 0.00095087 | 0.0017185 | 0.0 | 0.00
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Modify | 0.010187 | 0.011709 | 0.015284 | 1.9 | 0.03
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Other | | 0.09241 | | | 0.27
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Nlocal: 340 ave 344 max 334 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 4628 ave 4634 max 4624 min
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Histogram: 1 0 1 0 1 0 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: 66301.5 ave 67860 max 63963 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Total # of neighbors = 265206
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Ave neighs/atom = 195.004
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:33
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