130 lines
6.3 KiB
Groff
130 lines
6.3 KiB
Groff
LAMMPS (5 Jun 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../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 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 Bi_gr_AB_stack_2L_noH.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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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 = 0.000245051 secs
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read_data CPU = 0.00257704 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 layer1 molecule 1
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680 atoms in group layer1
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group layer2 molecule 2
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680 atoms in group layer2
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
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####################################################################
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pair_coeff * * rebo CH.rebo C 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 CH_taper.KC 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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#### Simulation settings ####
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timestep 0.001
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velocity all create 300.0 12345
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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 # REBO energy
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variable KC equal c_1 # total interlayer energy
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variable Evdw equal c_1[1] # attractive energy
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variable Erep equal c_1[2] # repulsive energy
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############################
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# Output
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thermo 100
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thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
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thermo_modify line one format float %.16f
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thermo_modify flush yes norm no lost warn
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###### Run molecular dynamics ######
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fix thermostat all nve
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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
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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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(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
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attributes: full, newton on, ghost
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 9.878 | 9.878 | 9.878 Mbytes
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Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
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0 0.0000000000000000 -10037.7640583250176860 -10090.4634194415175443 52.6993611164999933 -10057.1894932866325689 -33.2739261548851388 35.9559834317043467 -69.2299095866038954 299.9999999999999432
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100 1.5180600649910048 -10037.5122858156355505 -10065.4637593850711710 27.9514735694348637 -10032.2132655062741833 -33.2504938787968172 25.2100699046001573 -58.4605637833912795 159.1184768311167090
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200 3.0089348420733586 -10037.4414086674296414 -10061.6271012692577642 24.1856926018279914 -10028.9093252939601371 -32.7177759752976272 18.5366534598677504 -51.2544294351567515 137.6811336385757158
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300 4.5315427089808509 -10037.4824653300020145 -10064.2845326005372044 26.8020672705348311 -10030.9195389405158494 -33.3649936600211205 26.3639208740115549 -59.7289145340278722 152.5752876469494197
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400 6.0353655620710924 -10037.5105626329095685 -10064.8769084956238657 27.3663458627148124 -10031.8478821022818011 -33.0290263933414394 36.6142885774347562 -69.6433149707726074 155.7875386888504181
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500 7.5396006110822782 -10037.5010433784900670 -10064.8363209936269413 27.3352776151361780 -10031.4417172103858320 -33.3946037832416351 26.2980262321774489 -59.6926300154146787 155.6106774503813881
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600 9.2617433650884777 -10037.4817772372534819 -10064.1925798287848011 26.7108025915320830 -10031.4376178099319077 -32.7549620188514226 18.5745873777100208 -51.3295493965524017 152.0557480715018528
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700 10.7484918619738892 -10037.4834430268347205 -10064.1291975032127084 26.6457544763787268 -10030.8722888097836403 -33.2569086934306739 25.2322818106757047 -58.4891905041008613 151.6854507067412499
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800 12.2509897360578179 -10037.5047888097869873 -10064.8671187129039026 27.3623299031166667 -10031.9815058608728577 -32.8856128520297801 36.5236695083899718 -69.4092823604150908 155.7646771616151966
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900 13.7584852169966325 -10037.5068323939758557 -10065.3998155270637653 27.8929831330881477 -10032.1734374829648004 -33.2263780440982259 27.7314849391120788 -60.9578629832060841 158.7855101588031062
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1000 15.2755981830414385 -10037.4811494880432292 -10064.0099109142211091 26.5287614261777058 -10031.3325267421205353 -32.6773841721017888 18.9005970229946634 -51.5779811950868776 151.0194480395985295
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Loop time of 15.2757 on 4 procs for 1000 steps with 1360 atoms
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Performance: 5.656 ns/day, 4.243 hours/ns, 65.464 timesteps/s
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99.9% 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 | 13.985 | 14.446 | 14.823 | 7.9 | 94.57
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Bond | 0.00040979 | 0.00042456 | 0.00046059 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.43692 | 0.81428 | 1.2749 | 33.2 | 5.33
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Output | 0.00028016 | 0.00037143 | 0.00063561 | 0.0 | 0.00
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Modify | 0.0045586 | 0.0046468 | 0.0047903 | 0.1 | 0.03
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Other | | 0.01041 | | | 0.07
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Nlocal: 340 ave 340 max 340 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 4628 ave 4628 max 4628 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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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: 259250 ave 259250 max 259250 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1037000
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Ave neighs/atom = 762.5
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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: 0:00:15
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