190 lines
12 KiB
Plaintext
190 lines
12 KiB
Plaintext
LAMMPS (30 Nov 2020)
|
|
# Initialization
|
|
units metal
|
|
boundary p p p
|
|
atom_style charge
|
|
processors * * 1 # domain decomposition over x and y
|
|
|
|
# System and atom definition
|
|
# we use different molecule ids for each layer of hBN
|
|
# so that inter- and intra-layer
|
|
# interactions can be specified separately
|
|
read_data hBN-momolayer-5nm.data
|
|
Reading data file ...
|
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
880 atoms
|
|
read_data CPU = 0.005 seconds
|
|
mass 1 10.8110 # boron mass (g/mole) | membrane
|
|
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
|
|
|
######################## Potential defition ########################
|
|
pair_style tersoff shift 0.00
|
|
pair_coeff * * BNC.tersoff B N
|
|
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
|
####################################################################
|
|
# Neighbor update settings
|
|
neighbor 2.0 bin
|
|
neigh_modify every 1
|
|
neigh_modify delay 0
|
|
neigh_modify check yes
|
|
|
|
#### Simulation settings ####
|
|
timestep 0.001
|
|
#velocity all create 300.0 12345 loop geom
|
|
fix thermostat all nve
|
|
|
|
############# Output ###############
|
|
thermo 100
|
|
thermo_style custom step etotal pe ke temp
|
|
#thermo_modify lost warn
|
|
thermo_modify line one format float %20.16g lost warn
|
|
|
|
###### Run molecular dynamics ######
|
|
run 10000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 4.1
|
|
ghost atom cutoff = 4.1
|
|
binsize = 2.05, bins = 23 24 49
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair tersoff, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
|
|
Step TotEng PotEng KinEng Temp
|
|
0 -6551.83758440293 -6551.83758440293 0 0
|
|
100 -6551.840380657681 -6552.044977305669 0.2045966479884039 1.800715074874129
|
|
200 -6551.841530763759 -6552.090075168948 0.2485444051890892 2.187512168943174
|
|
300 -6551.841665139357 -6552.078462099445 0.2367969600872313 2.084119460928863
|
|
400 -6551.841676603799 -6552.08034358658 0.2386669827813768 2.100578078842757
|
|
500 -6551.841509448263 -6552.056119528737 0.214610080474919 1.888846229548393
|
|
600 -6551.84142207987 -6552.093343113157 0.2519210332867522 2.217230862663171
|
|
700 -6551.841781375172 -6552.084992531813 0.2432111566407525 2.140572685068615
|
|
800 -6551.842091951669 -6552.081838526557 0.2397465748869133 2.110079885437677
|
|
900 -6551.841666912234 -6552.080304400616 0.2386374883815078 2.100318489983454
|
|
1000 -6551.840715616244 -6552.05728371738 0.2165681011355425 1.906079343361184
|
|
1100 -6551.842074126828 -6552.106004260123 0.2639301332949162 2.322926472209997
|
|
1200 -6551.842188603395 -6552.098297277812 0.2561086744172286 2.254087519827168
|
|
1300 -6551.841260308251 -6552.048152704549 0.2068923962986277 1.820920628733306
|
|
1400 -6551.842388324547 -6552.124269628291 0.2818813037440244 2.480919985579661
|
|
1500 -6551.841440278005 -6552.064748455734 0.2233081777285259 1.965400733257461
|
|
1600 -6551.8417543223 -6552.076279064868 0.2345247425673758 2.064121008453587
|
|
1700 -6551.841597438737 -6552.076569576668 0.2349721379309549 2.068058666198944
|
|
1800 -6551.842162898317 -6552.070358112199 0.2281952138816812 2.008412971038309
|
|
1900 -6551.84187033836 -6552.097949414831 0.2560790764696407 2.253827019614037
|
|
2000 -6551.84242954704 -6552.100561654162 0.2581321071230393 2.271896344224688
|
|
2100 -6551.842712691072 -6552.109703914991 0.2669912239185734 2.349868028123894
|
|
2200 -6551.842406987503 -6552.121813176925 0.2794061894218752 2.459135778869765
|
|
2300 -6551.841269625166 -6552.048494026282 0.2072244011164852 1.823842700459919
|
|
2400 -6551.842117146576 -6552.084812413302 0.2426952667257221 2.136032186697286
|
|
2500 -6551.841419956284 -6552.050012185658 0.208592229374837 1.83588135792997
|
|
2600 -6551.842346075463 -6552.105596047079 0.263249971615804 2.316940169887984
|
|
2700 -6551.842399232389 -6552.124147695869 0.281748463480716 2.479750819481185
|
|
2800 -6551.842119881001 -6552.085857478666 0.2437375976646823 2.145206046842344
|
|
2900 -6551.842771389507 -6552.134521205791 0.291749816284512 2.567775657326773
|
|
3000 -6551.842975253373 -6552.140179022041 0.2972037686681092 2.615777491038857
|
|
3100 -6551.843221488605 -6552.150979194405 0.3077577057997783 2.708665785539887
|
|
3200 -6551.841490626381 -6552.051081317435 0.2095906910548411 1.84466911186702
|
|
3300 -6551.840943019135 -6552.052447647754 0.2115046286187543 1.861514237423045
|
|
3400 -6551.841023714494 -6552.077249795139 0.2362260806460777 2.079094983618369
|
|
3500 -6551.841577153114 -6552.077968261821 0.236391108706599 2.080547443955719
|
|
3600 -6551.842252635392 -6552.086062007893 0.2438093725005731 2.145837758213258
|
|
3700 -6551.842253480576 -6552.103458348384 0.2612048678080091 2.298940611769186
|
|
3800 -6551.841299048828 -6552.058453975489 0.21715492666169 1.911244166840182
|
|
3900 -6551.842314033157 -6552.097157445554 0.2548434123970678 2.242951577885938
|
|
4000 -6551.841574891869 -6552.082093672056 0.2405187801868552 2.116876290648488
|
|
4100 -6551.842382579084 -6552.079615297427 0.2372327183428749 2.087954697075952
|
|
4200 -6551.841658347794 -6552.086081658687 0.2444233108932888 2.15124120997885
|
|
4300 -6551.841497991208 -6552.04942232197 0.2079243307627577 1.830002986455737
|
|
4400 -6551.842107941061 -6552.10024928027 0.2581413392090596 2.271977598520067
|
|
4500 -6551.8422545168 -6552.111086664895 0.2688321480959159 2.366070541461399
|
|
4600 -6551.841904346708 -6552.101873923228 0.2599695765197279 2.288068451024916
|
|
4700 -6551.841053059403 -6552.066907635815 0.2258545764122718 1.987812334530229
|
|
4800 -6551.841371115727 -6552.053505472334 0.2121343566070521 1.867056658047954
|
|
4900 -6551.841937984535 -6552.109592091871 0.2676541073373525 2.355702259411726
|
|
5000 -6551.840851981332 -6552.044390859077 0.2035388777453223 1.791405328887585
|
|
5100 -6551.841070214648 -6552.067367827813 0.2262976131654189 1.991711630867481
|
|
5200 -6551.841571466906 -6552.093712758334 0.2521412914275312 2.21916941912714
|
|
5300 -6551.841486906651 -6552.072873466473 0.2313865598219879 2.036500942177379
|
|
5400 -6551.843256267483 -6552.145005653151 0.3017493856685349 2.655784798772142
|
|
5500 -6551.84270158117 -6552.134517274862 0.2918156936907907 2.568355463690886
|
|
5600 -6551.84163985875 -6552.056711349013 0.2150714902632286 1.892907232354023
|
|
5700 -6551.840381085197 -6552.022179207645 0.1817981224477595 1.600058568379124
|
|
5800 -6551.84149868601 -6552.080251188141 0.2387525021317378 2.101330759714621
|
|
5900 -6551.841216854843 -6552.0591162927 0.2178994378571792 1.917796828119392
|
|
6000 -6551.84110540275 -6552.060295375414 0.219189972664102 1.929155203265438
|
|
6100 -6551.841467351862 -6552.058791306032 0.2173239541699279 1.912731827489293
|
|
6200 -6551.841806857639 -6552.096852253635 0.255045395995332 2.244729294744194
|
|
6300 -6551.841325410201 -6552.081736713376 0.2404113031749354 2.115930353960526
|
|
6400 -6551.842446147665 -6552.103937221988 0.2614910743220556 2.30145959919854
|
|
6500 -6551.841597832866 -6552.080016016779 0.238418183913426 2.098388327072454
|
|
6600 -6551.840665386509 -6552.039901358558 0.1992359720502438 1.753534194501607
|
|
6700 -6551.841124220146 -6552.070638049088 0.2295138289419996 2.020018488725998
|
|
6800 -6551.841838744499 -6552.088979374696 0.2471406301962878 2.175157133725724
|
|
6900 -6551.841772926266 -6552.088344114766 0.2465711885006183 2.1701453104347
|
|
7000 -6551.84156512443 -6552.098852551235 0.2572874268055971 2.264462065139365
|
|
7100 -6551.842478978843 -6552.107722805476 0.265243826633506 2.334488672381989
|
|
7200 -6551.841537901573 -6552.094268243856 0.2527303422832519 2.22435382838405
|
|
7300 -6551.841978201499 -6552.098139567791 0.2561613662916175 2.254551276459881
|
|
7400 -6551.842490520111 -6552.108093934785 0.2656034146743838 2.337653512140213
|
|
7500 -6551.841813216483 -6552.0731438128 0.2313305963161162 2.036008390956932
|
|
7600 -6551.841416054815 -6552.07249289806 0.2310768432453098 2.03377503579501
|
|
7700 -6551.84270195916 -6552.135183767966 0.2924818088062866 2.574218138088869
|
|
7800 -6551.842416886451 -6552.114877572559 0.2724606861074197 2.398006368178555
|
|
7900 -6551.842013616702 -6552.083631656249 0.2416180395465499 2.126551194512558
|
|
8000 -6551.841352982264 -6552.048052020459 0.2066990381952127 1.819218827383714
|
|
8100 -6551.842271877219 -6552.119901127442 0.277629250222883 2.443496416083425
|
|
8200 -6551.841218957631 -6552.054157401546 0.2129384439153412 1.874133666160194
|
|
8300 -6551.841581833686 -6552.076372929738 0.2347910960514888 2.066465263546733
|
|
8400 -6551.841448567779 -6552.06355122901 0.2221026612302909 1.954790629168639
|
|
8500 -6551.840423567605 -6552.04780826226 0.2073846946551181 1.825253490882241
|
|
8600 -6551.841747604018 -6552.097807093885 0.2560594898680117 2.25365463219144
|
|
8700 -6551.843382701345 -6552.16148330718 0.3181006058349412 2.799696680690669
|
|
8800 -6551.843079858301 -6552.134975688002 0.2918958297006768 2.569060764205146
|
|
8900 -6551.842041173826 -6552.090533622544 0.2484924487182639 2.187054884812802
|
|
9000 -6551.841666657881 -6552.124145601612 0.2824789437309745 2.486179990298357
|
|
9100 -6551.841718135492 -6552.069395244891 0.2276771093996659 2.003852981613762
|
|
9200 -6551.842077607607 -6552.082979717109 0.2409021095014363 2.120250084316146
|
|
9300 -6551.842138891938 -6552.099457878667 0.257318986728701 2.264739833274149
|
|
9400 -6551.842439500782 -6552.134922812212 0.2924833114297478 2.574231363118433
|
|
9500 -6551.841065245899 -6552.07399886701 0.2329336211114915 2.050117082095376
|
|
9600 -6551.842249869504 -6552.08790605379 0.2456561842850767 2.162092090107294
|
|
9700 -6551.842315222852 -6552.104235020752 0.2619197978998719 2.305232921083908
|
|
9800 -6551.842195410218 -6552.108615477006 0.2664200667886112 2.344841106792793
|
|
9900 -6551.841488257895 -6552.075829625207 0.234341367311278 2.062507069069629
|
|
10000 -6551.841363981865 -6552.056912781978 0.2155488001135793 1.897108176266659
|
|
Loop time of 15.4494 on 1 procs for 10000 steps with 880 atoms
|
|
|
|
Performance: 55.924 ns/day, 0.429 hours/ns, 647.273 timesteps/s
|
|
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 15.071 | 15.071 | 15.071 | 0.0 | 97.55
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.11306 | 0.11306 | 0.11306 | 0.0 | 0.73
|
|
Output | 0.057197 | 0.057197 | 0.057197 | 0.0 | 0.37
|
|
Modify | 0.12765 | 0.12765 | 0.12765 | 0.0 | 0.83
|
|
Other | | 0.08016 | | | 0.52
|
|
|
|
Nlocal: 880.000 ave 880 max 880 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1518.00 ave 1518 max 1518 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0.00000 ave 0 max 0 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 15840.0 ave 15840 max 15840 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 15840
|
|
Ave neighs/atom = 18.000000
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:15
|