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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1 by 1 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 = 0.000143357 secs
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read_data CPU = 0.00128686 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) = 17.21 | 17.21 | 17.21 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 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589
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100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185
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200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970
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300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891
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400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571
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500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850
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600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380
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700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467
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800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011
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900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820
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1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202
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Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms
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Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
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100.0% CPU use with 1 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 | 53.836 | 53.836 | 53.836 | 0.0 | 99.90
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Bond | 0.00043479 | 0.00043479 | 0.00043479 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.032452 | 0.032452 | 0.032452 | 0.0 | 0.06
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Output | 0.00058326 | 0.00058326 | 0.00058326 | 0.0 | 0.00
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Modify | 0.0094135 | 0.0094135 | 0.0094135 | 0.0 | 0.02
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Other | | 0.009815 | | | 0.02
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Nlocal: 1360 ave 1360 max 1360 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 7964 ave 7964 max 7964 min
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Histogram: 1 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: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
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Histogram: 1 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: 0:00:54
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