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refactor code and examples to match LAMMPS conventions. whitespace cleanup. shorten examples.

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This commit is contained in:
Axel Kohlmeyer
2018-03-22 19:31:41 -04:00
parent 04c968362f
commit 8de7c449fc
29 changed files with 3542 additions and 5137 deletions
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228
examples/USER/misc/ilp_gr_hBN/bilayer-graphene/log.lmp
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@ -1,228 +0,0 @@
LAMMPS (5 Feb 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo ILP/graphene/hBN 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * ILP/graphene/hBN BNCH-old.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair ILP/graphene/hBN
variable REBO equal c_0
variable ILP equal c_1
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### 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 = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair ILP/graphene/hBN, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.39 | 12.39 | 12.39 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 0.0000000000000000 -5029.3801131277232344 -5044.0700799791011377 14.6899668513774859 -5011.2636297758563160 -32.8064502032452268 83.6251135126841376 22.0155657205247799 20.2812150219063234 3.4623630944674200 0.0282287194990573 0.0535565744690331 0.2193320108238477
100 1.2623029460082762 -5029.3895815657115236 -5045.3201249689691394 15.9305434032573761 -5012.4897058028163883 -32.8304191661527582 90.6873047362403781 22.0181751544732087 20.2867946176261533 3.4502536830854829 0.0239131348561319 0.0576557373214319 -0.4387830564309839
200 2.5089902369654737 -5029.3874064118581373 -5045.8119502227937119 16.4245438109355142 -5012.7276250747399899 -33.0843251480532530 93.4994853616529298 22.0202931358059395 20.2926890775462887 3.3883512918454923 0.0180268638923536 0.0596894423424165 -0.6964675465005062
300 3.7808456399943680 -5029.3851410393026526 -5044.9928147366936173 15.6076736973907035 -5012.1131531405408168 -32.8796615961530279 88.8493144891503590 22.0216852688933749 20.2985091182852351 3.3368274018412345 0.0093519892779965 0.0546775051020221 -0.2110676539008828
400 5.0828477439936250 -5029.3900102081943260 -5045.6706717598035539 16.2806615516088193 -5012.7330095297320440 -32.9376622300724975 92.6804113371579206 22.0220931528717330 20.3035219615837050 3.3560233852136392 -0.0015365116268860 0.0454268926971423 0.5478139708774018
500 6.3374099530046806 -5029.3985510532884291 -5046.0433160610555205 16.6447650077673792 -5013.0924334585288307 -32.9508826025281962 94.7531316611500074 22.0214795943650969 20.3074656871053847 3.4232399721971314 -0.0107212023950575 0.0332249365749148 0.6595923534430731
600 7.5914500529761426 -5029.3929936745525993 -5045.4367231194828491 16.0437294449299230 -5012.7046931021195633 -32.7320300173640391 91.3316353653480064 22.0200027175784747 20.3101652564580348 3.4651727437862387 -0.0178110391142554 0.0210056001697192 0.1144372537107130
700 8.8539019739837386 -5029.3934435811052026 -5045.6074608403341699 16.2140172592290135 -5012.7886962164220677 -32.8187646239108304 92.3010274643678201 22.0178838793005234 20.3116257076998501 3.4432436715031316 -0.0242636236518299 0.0078323423535019 -0.5162836954824445
800 10.1049926480045542 -5029.3892931255340955 -5046.2270462379728997 16.8377531124386870 -5013.2383770824435487 -32.9886691555297418 95.8517489911287015 22.0151485190623291 20.3116305041057075 3.3780520461370140 -0.0302821177574879 -0.0083184718697242 -0.6710801514935791
900 11.3630027609760873 -5029.3930414671476683 -5046.0272003817681252 16.6341589146203184 -5013.2317798383628542 -32.7954205434054487 94.6927546873744745 22.0119224939835121 20.3099187654038786 3.3350551183455268 -0.0341747588450106 -0.0256858065985706 -0.0799872839190919
1000 12.6231660830089822 -5029.3908907830582393 -5045.6437703691590286 16.2528795861005300 -5012.6800867884940089 -32.9636835806647710 92.5222578135494871 22.0084902521404544 20.3065746721438387 3.3658243730415687 -0.0336536244697077 -0.0406018547138186 0.6191660973820151
1100 13.8672335039591417 -5029.3936273537710804 -5045.9027321589628627 16.5091048051920097 -5012.9359164310717460 -32.9668157278903138 93.9808630812208889 22.0052717045119905 20.3019474054695905 3.4333328890827421 -0.0306983142305894 -0.0504731478622083 0.5931965879862887
1200 15.1198259049560875 -5029.3940797064951767 -5045.6377384352035733 16.2436587287087058 -5012.8554686686165951 -32.7822697665871203 92.4697665279069270 22.0023306815922979 20.2966557735895385 3.4659529127677287 -0.0274706885173217 -0.0547501807332978 0.0091573603413281
1300 16.3654009730089456 -5029.3984566732624444 -5045.6895616381252694 16.2911049648628570 -5012.7356994597503217 -32.9538621783744219 92.7398622282092333 21.9998860754741905 20.2910565803948018 3.4345399235545337 -0.0213260369994740 -0.0568287466574244 -0.5888067543760942
1400 17.6155319709796458 -5029.3815168178471140 -5045.2912598742987029 15.9097430564518749 -5012.3239955600220128 -32.9672643142766546 90.5688952544279573 21.9981598497936552 20.2854554509222993 3.3672595338608167 -0.0132303590611009 -0.0543234153355907 -0.6236559250459623
1500 18.8714692159555852 -5029.3921017874845347 -5045.6708613750924997 16.2787595876079862 -5012.8369791315399198 -32.8338822435533757 92.6695840863495306 21.9974041415691559 20.2802681532087163 3.3352413807666181 -0.0014089849714996 -0.0481849064168331 0.0587582898344604
1600 20.1541873109526932 -5029.3874846931976208 -5045.7731643864972284 16.3856796932995650 -5012.8388777565696728 -32.9342866299264614 93.2782448182427402 21.9977706803512874 20.2759915865795222 3.3762928385876232 0.0085254010295789 -0.0376205539327122 0.6681442617907806
1700 21.4234082509647124 -5029.3869010344951676 -5045.3169437830329116 15.9300427485373124 -5012.4635360220827351 -32.8534077609500770 90.6844546748195768 21.9990330035990027 20.2727720473957298 3.4424374239173727 0.0168149635384655 -0.0269413439785030 0.5265928985608515
1800 22.6835704990080558 -5029.3860480733746954 -5045.4015510274330154 16.0155029540583165 -5012.6540263485476316 -32.7475246788853056 91.1709513061473160 22.0010236218414903 20.2706889597509488 3.4653364051690918 0.0229089788849714 -0.0142749791424698 -0.1062662269544749
1900 23.9297129529877566 -5029.3992153438584864 -5046.0849535192628537 16.6857381754043104 -5013.1667872952384641 -32.9181662240248301 94.9863783273459319 22.0036010850046679 20.2699115012928246 3.4242520686326885 0.0283626891504371 -0.0012584790958115 -0.6446526361083699
2000 25.1922093119937927 -5029.3947678008062212 -5046.0655253357617767 16.6707575349551895 -5013.1017054839030607 -32.9638198518594550 94.9010985053609772 22.0065845205626758 20.2704964280075011 3.3582948439944240 0.0313750540289036 0.0137999047920244 -0.5449451253646518
2100 26.4518803840037435 -5029.3820643301123710 -5045.4331743009661295 16.0511099708533358 -5012.5538273606616713 -32.8793469403044938 91.3736502537662716 22.0097398064544976 20.2727372928018958 3.3379848824292826 0.0322718100086602 0.0304537099550799 0.1867563300323286
2200 27.7058059349656105 -5029.3843727776211381 -5045.0848436909873271 15.7004709133658302 -5012.0668628677258312 -33.0179808232617233 89.3775782897492945 22.0127920131602473 20.2765354452670756 3.3881998421430568 0.0292294495100443 0.0449660178787396 0.7042838989885432
2300 28.9594137629610486 -5029.3902199294761886 -5045.3993732492435811 16.0091533197674920 -5012.5253283328802354 -32.8740449163632320 91.1348049421897599 22.0155716600061417 20.2815245415556973 3.4510500976839618 0.0259484063993953 0.0538549628124416 0.4400016714913355
2400 30.2447868830058724 -5029.3940355103695765 -5045.9434469962816365 16.5494114859119250 -5013.1710648528805905 -32.7723821434015932 94.2103156582501100 22.0179797175199319 20.2871333501902136 3.4632861236609225 0.0218917592723929 0.0581043349886307 -0.2124896915144417
2500 31.5081150379846804 -5029.3842094590991110 -5045.4423687097469156 16.0581592506475950 -5012.4554219817418925 -32.9869467280046536 91.4137794677353384 22.0198491689972187 20.2929823072195745 3.4144243213892453 0.0156275666670157 0.0584945195169434 -0.6844296511643093
2600 32.7705356059595942 -5029.3960582840263669 -5045.6469174766025390 16.2508591925761650 -5012.8198838898442773 -32.8270335867577927 92.5107563827072994 22.0210406125338700 20.2986562400797226 3.3502383230453026 0.0082866848267277 0.0535700449402662 -0.4533139815189942
2700 34.0687214930076152 -5029.4005011063927668 -5046.1812481784818374 16.7807470720886371 -5013.3384539147527903 -32.8427942637283650 95.5272324933440444 22.0214074387511722 20.3035983394416988 3.3422072391285718 -0.0010968873414058 0.0448881856269352 0.3053226005544524
2800 35.3371960269869305 -5029.3918450884730191 -5045.4663013118542949 16.0744562233815529 -5012.5518420452062855 -32.9144592666481230 91.5065527332286166 22.0208057886537567 20.3075286333744920 3.3990332666058265 -0.0107042888216099 0.0331308854628973 0.7104765178449446
2900 36.5826528539764695 -5029.4007271172231412 -5046.3887404126471665 16.9880132954239791 -5013.5657268280101562 -32.8230135846359303 96.7071304215778440 22.0193692100171923 20.3101603808999265 3.4577797292506842 -0.0181908513743875 0.0197672476938271 0.3528489229883396
3000 37.8225702039781027 -5029.3940496855184392 -5045.4382560043904959 16.0442063188722450 -5012.6853249922505711 -32.7529310121395909 91.3343500506812944 22.0171604936519856 20.3114668671039951 3.4591467250701471 -0.0250556884411515 0.0058380040945131 -0.3232243449560073
3100 39.1152549439575523 -5029.3932299425177916 -5045.7076145083992742 16.3143845658812481 -5012.7273205114888697 -32.9802939969102908 92.8723852827122727 22.0144106189674247 20.3113170196305575 3.4036898869224110 -0.0295489605326196 -0.0093545138913292 -0.6945887338714194
3200 40.3652645039837807 -5029.3999346652944951 -5046.2743567265588354 16.8744220612639957 -5013.3523379216176181 -32.9220188049421125 96.0604931659067063 22.0112657104147473 20.3096089828088715 3.3446022440995744 -0.0331585594875426 -0.0245083162220922 -0.3611700155337798
3300 41.7497809809865430 -5029.3912545533439697 -5045.6188249698325308 16.2275704164882058 -5012.7210368537616887 -32.8977881160708634 92.3781810975735169 22.0079411449246116 20.3062958566965044 3.3478683972107479 -0.0330599183649122 -0.0412983807445889 0.4228102245782292
3400 43.0772461489541456 -5029.3913786027551396 -5045.6933303802852606 16.3019517775300287 -5012.6836451483668498 -33.0096852319176293 92.8016095384462147 22.0046876041177768 20.3016343021786838 3.4103619804324348 -0.0302848635086505 -0.0508933045183329 0.6902755158347326
3500 44.3340892840060405 -5029.3864373789210731 -5044.9075681866406740 15.5211308077191479 -5012.1156930534052663 -32.7918751332351519 88.3566544957194822 22.0018906600734354 20.2961922297910284 3.4617631548194869 -0.0260020821660879 -0.0574179239791507 0.2536077963142296
3600 45.5714052729890682 -5029.3956106765108416 -5045.8281093106388653 16.4324986341276862 -5013.0062724883737246 -32.8218368222655954 93.5447695341190126 21.9995902792937201 20.2903196955397753 3.4528875370982139 -0.0198574899622142 -0.0590999812510351 -0.4161058838372516
3700 46.8187310720095411 -5029.3999849462825296 -5045.8608125716009454 16.4608276253185934 -5012.9301564107845479 -32.9306561608159001 93.7060370936722506 21.9980000204408341 20.2845522706275894 3.3917483074441592 -0.0115465621905488 -0.0553944579545257 -0.6931324325703953
3800 48.0849941459600814 -5029.3934499086271899 -5045.0668678198253474 15.6734179111983085 -5012.2357009255956655 -32.8311668942298382 89.2235745128853779 21.9973189064792436 20.2792712394156425 3.3397277035718815 -0.0020664024879512 -0.0492333401974764 -0.2331021270184729
3900 49.3429405399947427 -5029.3995770528044886 -5046.0950053993201436 16.6954283465152358 -5013.2247015792199818 -32.8703038200997284 95.0415412604762082 21.9976186964129639 20.2749399452365466 3.3551882655200593 0.0084267344129547 -0.0373784583523626 0.5086238489046713
4000 50.5998689539846964 -5029.3888468870900397 -5045.4588592431082361 16.0700123560180224 -5012.5056530215588282 -32.9532062215491379 91.4812552688796359 21.9989183465402434 20.2718151808636300 3.4207597363868252 0.0165850539989395 -0.0251757999596484 0.6640462831884847
4100 51.8629528660094365 -5029.3910837396306306 -5045.2793764258776719 15.8882926862469578 -5012.4770743669359945 -32.8023020589422742 90.4467854047990585 22.0009590702850808 20.2699385934667973 3.4644847478947058 0.0233393143572127 -0.0117891349194484 0.1342112403658827
4200 53.1236869489657693 -5029.3984010758495060 -5046.2448879520343326 16.8464868761852031 -5013.3818327446442709 -32.8630552073907438 95.9014674140553467 22.0035487123982918 20.2693875306188644 3.4447945125877593 0.0282346202644504 0.0006576204547461 -0.4934516926995214
4300 54.3830584579845890 -5029.3974364654013698 -5045.8912824487397302 16.4938459833379767 -5012.8566186763018777 -33.0346637724379022 93.8939996646779349 22.0065160962032245 20.2702208441870937 3.3813367869591255 0.0318644587592501 0.0164543727145067 -0.6628252924648856
4400 55.6534237450105138 -5029.3926368191096117 -5045.2218371804192429 15.8292003613099244 -5012.3457495788206870 -32.8760876015986199 90.1103923801868518 22.0096837224699016 20.2727742192121454 3.3372739454265710 0.0314356050658150 0.0335424174115672 -0.1161529061464756
4500 56.9183939939830452 -5029.3940454417834189 -5045.9258580870837250 16.5318126453004588 -5012.9929638810244796 -32.9328942060604319 94.1101312903264073 22.0128271345169999 20.2768840530886756 3.3637778632090720 0.0302602474720397 0.0485668445849368 0.5881899043646754
4600 58.1842329019564204 -5029.3897931061719646 -5045.3405006579350811 15.9507075517634878 -5012.4008178333297110 -32.9396828246052280 90.8020925519495847 22.0156613833127963 20.2821435957056515 3.4302716374285005 0.0260054978861435 0.0562442375978452 0.6083123358868219
4700 59.4382298499695025 -5029.3969593583269670 -5045.7810386931287212 16.3840793348014095 -5013.0572476947481846 -32.7237909983807498 93.2691345076189435 22.0180314970645661 20.2879823773636403 3.4648846252063747 0.0214335018843589 0.0598518189522713 0.0304394820826928
4800 60.6967262169928290 -5029.3856671230942084 -5045.3017305595958533 15.9160634365015543 -5012.4665014359597990 -32.8352291236367648 90.6048750836845613 22.0199625290182688 20.2941047508438963 3.4363593409545792 0.0167963433674092 0.0615833915650458 -0.5541548942758866
4900 61.9512241869815625 -5029.3923848959475436 -5045.7384583560833562 16.3460734601355888 -5012.7852573671316350 -32.9532009889525597 93.0527796570441836 22.0212592278909085 20.3000537186652821 3.3718475316480969 0.0086391048459562 0.0563118558122456 -0.6148391029712286
5000 63.2058322129887529 -5029.3915775167406537 -5045.1695079529654322 15.7779304362247856 -5012.3445352609178371 -32.8249726920481351 89.8185296858452773 22.0217142875197673 20.3052386826657560 3.3368855121137573 -0.0005848472434748 0.0469229219675754 -0.0025464403573191
5100 64.4612582869594917 -5029.3892459301187046 -5045.4092843740309036 16.0200384439126253 -5012.4115638930270507 -32.9977204810038813 91.1967703469756117 22.0211363551768393 20.3092236811018836 3.3731385391734987 -0.0104558693316052 0.0318306688289283 0.6399924297249336
5200 65.7134019279619679 -5029.4030454404182819 -5046.2627024036355579 16.8596569632174536 -5013.2682522266104570 -32.9944501770255414 95.9764403553959653 22.0196975554592207 20.3116344765031158 3.4385226880437783 -0.0183768904268109 0.0160982826367598 0.5345362236176538
5300 66.9578059059567750 -5029.3919597195299502 -5045.5335222071535100 16.1415624876236983 -5012.7301328351986740 -32.8033893719546015 91.8885664587487412 22.0175315555966975 20.3126154236309091 3.4630139347774884 -0.0242754059642420 0.0032173312250643 -0.0775763877645290
5400 68.2489708719658665 -5029.3846231466677636 -5045.4515583416805384 16.0669351950124017 -5012.5148025922717352 -32.9367557494093148 91.4637380109446525 22.0148268891839543 20.3122214814806945 3.4262265154739362 -0.0300322552067342 -0.0114101644224351 -0.5957408015264980
5500 69.5872814320027828 -5029.3976079434123676 -5046.2615016619420203 16.8638937185299866 -5013.2875337165860401 -32.9739679453564989 96.0005587994687488 22.0116064706776839 20.3102420050743042 3.3624439592830382 -0.0331793464510278 -0.0273205776972141 -0.5547024024481256
5600 71.0810253079980612 -5029.3990311253737673 -5046.3786084092271267 16.9795772838533381 -5013.5810569834520720 -32.7975514257743583 96.6591070031231538 22.0082577080594533 20.3067263674726988 3.3382716477917813 -0.0327038891431524 -0.0431208290112252 0.1347255325181367
5700 72.4856253899633884 -5029.3926984710069519 -5045.4056210227572592 16.0129225517498952 -5012.4766481517817738 -32.9289728709757838 91.1562619308659805 22.0050646686591129 20.3018397290024808 3.3836722937755463 -0.0302272076858413 -0.0535767293433688 0.6666043489739104
5800 73.8634844649932347 -5029.3834029837780690 -5045.1129758304869029 15.7295728467090985 -5012.2694155058643446 -32.8435603246219827 89.5432459528482951 22.0022483685200818 20.2961021426530372 3.4452080928763542 -0.0254277345115299 -0.0599208650276596 0.4504328249672133
5900 75.3915032909717411 -5029.3974484823693274 -5045.9428387883463074 16.5453903059766532 -5013.1858688276588509 -32.7569699606872575 94.1874244133654770 21.9999199731949346 20.2899812203382055 3.4600553052011818 -0.0206282083304644 -0.0609517769948545 -0.1746052875828525
6000 76.6400258549838327 -5029.3913152258628543 -5045.4435744126367354 16.0522591867739663 -5012.4608078601768284 -32.9827665524597151 91.3801923591900334 21.9982238811128710 20.2840090111223468 3.4161665208076437 -0.0125595347519585 -0.0579440096045873 -0.6333327422350389
6100 77.8959925099625252 -5029.3932757362208577 -5045.8790782711030261 16.4858025348824633 -5012.8969642404263141 -32.9821140306764420 93.8482109779551621 21.9973730537864682 20.2785476188032163 3.3549557462646411 -0.0042410493519084 -0.0506002459180393 -0.4680789345019807
6200 79.1497183470055461 -5029.4088636981850868 -5046.6649961249258922 17.2561324267410470 -5013.7231617170655227 -32.9418344078599077 98.2334437902978976 21.9974997583151222 20.2740486557909172 3.3425028819702134 0.0059955322593470 -0.0383588614992616 0.2484046320153767
6300 80.4047899909783155 -5029.3923725331251262 -5045.8449198462867571 16.4525473131614497 -5012.7774496031424860 -33.0674702431445411 93.6589000203849338 21.9985309965303522 20.2709033994038990 3.3945366047562309 0.0146161778945059 -0.0238717757127838 0.6755315511238056
6400 81.6621199259534478 -5029.3873259574293115 -5045.4805995313954554 16.0932735739664388 -5012.6101575755155864 -32.8704419558798833 91.6136736746568658 22.0004178415001554 20.2692296192343555 3.4515126206720894 0.0224924238087105 -0.0095626954394393 0.3649317751543234
6500 82.9068036190001294 -5029.3885153625169551 -5045.6513413124866929 16.2628259499700896 -5012.8502848348771295 -32.8010564776094071 92.5788791671608067 22.0028744822954785 20.2690295011692143 3.4565824273753738 0.0266893593346073 0.0051394765466491 -0.2690238272862540
6600 84.1584947239607573 -5029.3921990608459964 -5045.6152780635047748 16.2230790026588494 -5012.6733651291715432 -32.9419129343335868 92.3526129669499198 22.0057446397104144 20.2703054065310688 3.4059684940340356 0.0301975147648949 0.0206588430605317 -0.6562141768091865
6700 85.5309034659876488 -5029.3958221014900118 -5045.9855980438351253 16.5897759423451419 -5013.1614032626457629 -32.8241947811894832 94.4400971332701857 22.0088155297199890 20.2731431317838826 3.3483252260002931 0.0305868287843257 0.0360401338403821 -0.3706227597734457
6800 86.7887097629718482 -5029.3989256161685262 -5046.1660314126675075 16.7671057964989494 -5013.3811893242827864 -32.7848420883840248 95.4495772316823547 22.0117933253442750 20.2774465117832499 3.3473285762193563 0.0293264534798696 0.0498605326239532 0.3567087933199659
6900 88.0344084189855494 -5029.3894635412279968 -5045.3755615873205898 15.9860980460924917 -5012.4313435990561629 -32.9442179882648674 91.0035589089179382 22.0145527278245225 20.2830023561391073 3.4048481829747144 0.0261339472632872 0.0603043040288190 0.6629381496962342
7000 89.2877694109920412 -5029.3931851776624171 -5046.2660855250323948 16.8729003473701340 -5013.4206101329300509 -32.8454753921025357 96.0518305529549394 22.0169018761537423 20.2892381473745935 3.4563764158029811 0.0215256303139502 0.0635714094149741 0.2735262616382870
7100 90.5343435019603930 -5029.3943719418657565 -5045.8063859927260637 16.4120140508601793 -5012.9341376927177407 -32.8722483000083230 93.4281575894947309 22.0187504680106265 20.2956576132647477 3.4511897261914934 0.0151769557575876 0.0638586358909771 -0.3697827551013745
7200 91.7890073219896294 -5029.3882574016588478 -5045.6074919269822203 16.2192345253231593 -5012.5576675194106429 -33.0498244075712222 92.3307276314112642 22.0199381323646897 20.3017542818957075 3.3949190800948910 0.0083746540157601 0.0572124597101438 -0.6554142442507734
7300 93.0481603289954364 -5029.3919256510280320 -5045.3161120841996308 15.9241864331714869 -5012.3304308333417794 -32.9856812508580077 90.6511166120323679 22.0203434199504891 20.3069201065105531 3.3436661088988298 -0.0008082605025240 0.0457808438470512 -0.2589589418874469
7400 94.2895189719856717 -5029.3973426785032643 -5045.6621408997361868 16.2647982212324713 -5012.7648025615653751 -32.8973383381705773 92.5901066539116755 22.0197952390567870 20.3107436357954469 3.3541554622638241 -0.0103306966484018 0.0301663424617996 0.4552583449586026
7500 95.5377785899909213 -5029.3948467570653520 -5045.7331434291627374 16.3382966720969520 -5012.7514741351296834 -32.9816692940330185 93.0085089797121896 22.0182835442860032 20.3129031135621219 3.4158962237430512 -0.0195959596334220 0.0135047192390157 0.6456073746637249
7600 96.8022272579837590 -5029.3931838808439352 -5045.4289963141181943 16.0358124332747032 -5012.6277589903447733 -32.8012373237726393 91.2865664414322850 22.0159526773315513 20.3134816232245754 3.4596215546593516 -0.0265035067457815 -0.0018448570141999 0.1605592216624496
7700 98.0480918029788882 -5029.3927224394574296 -5045.5505410460209532 16.1578186065634384 -5012.7503911560907000 -32.8001498899307080 91.9811071571291450 22.0130792027109443 20.3125442860891496 3.4436146964093655 -0.0310809711922193 -0.0174733457478587 -0.4479487784855753
7800 99.2981190299615264 -5029.4031547353506539 -5046.1752453778135532 16.7720906424625866 -5013.2528054902131771 -32.9224398875998361 95.4779543079392141 22.0098273587463140 20.3100791980582827 3.3840076444806408 -0.0342478030204245 -0.0319633867573659 -0.6355009600038708
7900 100.5537567089777440 -5029.3944791921421711 -5044.9960502255426036 15.6015710334007611 -5012.1309422092845125 -32.8651080162585743 88.8145740452778938 22.0064004970442220 20.3061392621748453 3.3408200783635791 -0.0334515103138912 -0.0469088387662372 -0.1361992518732273
8000 101.8002213349682279 -5029.3929935269861744 -5045.6154036718935458 16.2224101449071263 -5012.6903925591586813 -32.9250111127354685 92.3488053814068479 22.0031954529123475 20.3008903778718448 3.3630664386411944 -0.0303145741127793 -0.0573027579844121 0.5298234484194294
8100 103.0604241339606233 -5029.3895181224415865 -5045.5242483757247101 16.1347302532831307 -5012.5130106423803227 -33.0112377333444016 91.8496728126257977 22.0004617169451784 20.2948581865125668 3.4259829025735637 -0.0235597360754076 -0.0625047587166574 0.5944988997279915
8200 104.3003088539699093 -5029.3921128333386150 -5045.3442595710002934 15.9521467376618311 -5012.4679081513959318 -32.8763514196039210 90.8102853603699458 21.9984673460497753 20.2885772435489642 3.4606217876185612 -0.0159679066697783 -0.0624611171154739 0.0390314113354409
8300 105.5484032649546862 -5029.3877455487827319 -5045.0575951302926114 15.6698495815094372 -5012.1517525987401314 -32.9058425315530698 89.2032611943938178 21.9972613261819880 20.2824755664924403 3.4344648587864106 -0.0085123036477869 -0.0597425423571583 -0.5144098325620685
8400 106.7977103599696420 -5029.3940956297292360 -5045.7712194348414414 16.3771238051123973 -5012.7148337952312431 -33.0563856396105251 93.2295389819333309 21.9968254159544792 20.2768205630926097 3.3742357039982664 0.0005515507797924 -0.0525489103533247 -0.5831587742081521
8500 108.0498831009608693 -5029.3966688220943979 -5045.9181006527742284 16.5214318306794148 -5013.1123929561299519 -32.8057076966441983 94.0510367525495781 21.9973649793415653 20.2722228282212278 3.3398553423288360 0.0104639615307145 -0.0388449586124005 -0.0141990665176662
8600 109.3168672239989974 -5029.3901274034988091 -5045.9375078140647020 16.5473804105655624 -5012.9853021568969780 -32.9522056571671698 94.1987534193348921 21.9989049134571175 20.2690982462850933 3.3731313497904591 0.0192133927474549 -0.0232345679884083 0.5999078241684682
8700 110.5636035219649784 -5029.3901389215689051 -5045.6376930378537509 16.2475541162848280 -5012.7481174817003193 -32.8895755561536873 92.4919416785743636 22.0011367928294845 20.2675706259688049 3.4350238082277742 0.0251426611885136 -0.0075450321086530 0.5206167046178872
8800 111.8004809370031580 -5029.3924574370830669 -5045.1157123468474310 15.7232549097647301 -5012.3693783131229793 -32.7463340337239828 89.5072800313806596 22.0038756926631685 20.2674918694414608 3.4599837012727228 0.0287406400340964 0.0054631832109070 -0.0593929995926347
8900 113.0429552759742364 -5029.3987474982423009 -5046.0489177048530109 16.6501702066103476 -5013.1575753877641546 -32.8913423170885579 94.7839016670577763 22.0068663666915683 20.2687690591312801 3.4257808041439497 0.0309099788432120 0.0202171302469460 -0.5672379170296111
9000 114.3028285600012168 -5029.3950511511229706 -5045.5452299460939685 16.1501787949714100 -5012.5755502794254426 -32.9696796666691085 91.9376162413181817 22.0100025642331438 20.2715213988307390 3.3652959904269899 0.0310727498337748 0.0350587744467375 -0.5243423250951003
9100 115.5504704579943791 -5029.4011682817399560 -5045.7686964972572241 16.3675282155176056 -5012.8956927574890869 -32.8730037397681514 93.1749144700332010 22.0129932323966244 20.2757847863275558 3.3416863642298322 0.0278865835662406 0.0500593574538005 0.1106488240215337
9200 116.7946333579602651 -5029.4017720229812767 -5046.2095242659142968 16.8077522429334536 -5013.1790196502061008 -33.0305046157081676 95.6809639823375306 22.0155766145636562 20.2813847767229340 3.3837475995761923 0.0229459653959643 0.0606619684052993 0.6316843785669454
9300 118.0373532379744574 -5029.3897983703673162 -5045.3852343116877819 15.9954359413206522 -5012.4098851963299239 -32.9753491153576448 91.0567164521802823 22.0176661603918404 20.2876093495490188 3.4433051081136128 0.0182119330164441 0.0630872424142740 0.4408646538230431
9400 119.3096107059973292 -5029.3940044671780925 -5045.1494022809556554 15.7553978137776411 -5012.3373351985219415 -32.8120670824327760 89.6902589328241930 22.0191620625590261 20.2939150847352963 3.4576781527342213 0.0120237458614373 0.0624136446207651 -0.1706807559293053
9500 120.5569760259822942 -5029.4028547635489304 -5046.4916138968292216 17.0887591332807105 -5013.5750575302763536 -32.9165563665534435 97.2806430926366943 22.0200362005428580 20.2999278998203252 3.4154427529782021 0.0047438742484681 0.0566484545204492 -0.6003708189460565
9600 121.8032315599848516 -5029.3943080876824752 -5045.8625616630897639 16.4682535754077222 -5012.9435173518513693 -32.9190443112383448 93.7483105668138563 22.0201112440302111 20.3051306661589130 3.3573333481987917 -0.0034848828375071 0.0463786363566361 -0.4464499679272487
9700 123.0481046040076762 -5029.3963743848999002 -5046.0931232530328998 16.6967488681334011 -5013.3188208671426764 -32.7743023858902305 95.0490585524709672 22.0192892506256435 20.3090481568511585 3.3449646688919508 -0.0126993251202254 0.0313153276927252 0.2347902151897416
9800 124.3171976699959487 -5029.4041067798116273 -5046.2351730935588421 16.8310663137475451 -5013.3022700315450493 -32.9329030620125565 95.8136832619653376 22.0176816744773589 20.3113320548697089 3.3948762489105730 -0.0190003685475649 0.0145775023377736 0.6452872225841749
9900 125.6034698109724559 -5029.3967328994849595 -5045.7044510326986710 16.3077181332140952 -5012.8792223601285514 -32.8252286725705744 92.8344354905748617 22.0154641674261171 20.3119427417383847 3.4494353673823004 -0.0251076944963040 -0.0022494305485361 0.3449321806936739
10000 126.8703936609672382 -5029.3954046432463656 -5045.6299775343904912 16.2345728911443530 -5012.8287818160133611 -32.8011957183766398 92.4180438654010175 22.0127364302381388 20.3109725422284022 3.4537555828445510 -0.0290125415995836 -0.0167131954412302 -0.2644721653229455
Loop time of 126.87 on 4 procs for 10000 steps with 1360 atoms
Performance: 6.810 ns/day, 3.524 hours/ns, 78.821 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 117.02 | 119.45 | 123.17 | 21.1 | 94.15
Bond | 0.0041073 | 0.0042996 | 0.004639 | 0.3 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 3.4989 | 7.2187 | 9.6549 | 85.7 | 5.69
Output | 0.013072 | 0.013851 | 0.016114 | 1.1 | 0.01
Modify | 0.060992 | 0.063045 | 0.065171 | 0.8 | 0.05
Other | | 0.1165 | | | 0.09
Nlocal: 340 ave 344 max 334 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 4628 ave 4634 max 4624 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 66301.5 ave 67860 max 63963 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:06

1162
examples/USER/misc/ilp_gr_hBN/gr-hBN/log.lmp
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1159
examples/USER/misc/ilp_gr_hBN/log.lmp
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1
examples/USER/misc/ilp_graphene_hbn/BNC.tersoff Symbolic link
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@ -0,0 +1 @@
../../../../potentials/BNC.tersoff

1
examples/USER/misc/ilp_graphene_hbn/BNCH-old.ILP Symbolic link
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@ -0,0 +1 @@
../../../../potentials/BNCH-old.ILP

1
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/BNCH-old.ILP

0
examples/USER/misc/ilp_gr_hBN/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data → examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data
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1
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/CH.airebo

16
examples/USER/misc/ilp_gr_hBN/bilayer-graphene/in.bilayer-graphene → examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene
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@ -16,10 +16,10 @@ group membrane type 1
group adsorbate type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ILP/graphene/hBN 16.0
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
pair_coeff * * ILP/graphene/hBN BNCH-old.ILP C C # long range
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
@ -42,7 +42,7 @@ fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair ILP/graphene/hBN
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0
variable ILP equal c_1
@ -50,12 +50,12 @@ variable ILP equal c_1
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.16f
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn
dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 10000
run 1000

137
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1 Normal file
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0
variable ILP equal c_1
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564
200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465
300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539
400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113372 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709
500 -5029.3985510533 -5046.0433160610 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534
600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537
700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274644 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955
800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515
900 -5029.3930414672 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839
1000 -5029.3908907831 -5045.6437703691 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974
Loop time of 137.46 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.629 ns/day, 38.183 hours/ns, 7.275 timesteps/s
95.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 137.33 | 137.33 | 137.33 | 0.0 | 99.90
Bond | 0.00071788 | 0.00071788 | 0.00071788 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.067907 | 0.067907 | 0.067907 | 0.0 | 0.05
Output | 0.0016029 | 0.0016029 | 0.0016029 | 0.0 | 0.00
Modify | 0.036542 | 0.036542 | 0.036542 | 0.0 | 0.03
Other | | 0.02574 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 265206 ave 265206 max 265206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:17

137
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4 Normal file
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@ -0,0 +1,137 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0
variable ILP equal c_1
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564
200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465
300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539
400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113371 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709
500 -5029.3985510533 -5046.0433160611 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534
600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537
700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274643 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955
800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515
900 -5029.3930414671 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839
1000 -5029.3908907831 -5045.6437703692 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974
Loop time of 36.0917 on 4 procs for 1000 steps with 1360 atoms
Performance: 2.394 ns/day, 10.025 hours/ns, 27.707 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.204 | 34.289 | 35.893 | 17.3 | 95.01
Bond | 0.00038719 | 0.00065947 | 0.00097609 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.1539 | 1.7595 | 2.8464 | 76.7 | 4.88
Output | 0.0013447 | 0.0014529 | 0.0016887 | 0.4 | 0.00
Modify | 0.010811 | 0.012037 | 0.013764 | 1.0 | 0.03
Other | | 0.0287 | | | 0.08
Nlocal: 340 ave 344 max 334 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 4628 ave 4634 max 4624 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 66301.5 ave 67860 max 63963 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:36

1
examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/BNC.tersoff

1
examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/BNCH-old.ILP

1
examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/CH.airebo

0
examples/USER/misc/ilp_gr_hBN/gr-hBN/gr_hBN_Cstack_2L_noH.data → examples/USER/misc/ilp_graphene_hbn/gr-hBN/gr_hBN_Cstack_2L_noH.data
View File

16
examples/USER/misc/ilp_gr_hBN/gr-hBN/in.grhBN → examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN
View File

@ -16,11 +16,11 @@ group membrane type 1 2
group adsorbate type 3
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ILP/graphene/hBN 16.0 coul/shield 16.0
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
pair_coeff * * ILP/graphene/hBN BNCH-old.ILP B N C # long range
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
@ -46,7 +46,7 @@ fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ILP/graphene/hBN
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
@ -61,11 +61,11 @@ variable Evdw equal c_sldsub
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.16f
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 100000
run 1000

171
examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1 Normal file
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@ -0,0 +1,171 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
720 atoms in group membrane
group adsorbate type 3
720 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2
variable Ecoul equal c_3
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
7 neighbor lists, perpetual/occasional/extra = 6 1 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (6)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) compute group/group, occasional, copy from (7)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(7) neighbor class addition, perpetual, half/full from (6)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -10708.4531746010 -10764.2547791975 55.8016045965 -66.8250335416 -5401.7347845703 -5322.2780762734 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755
100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614
200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321
300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196
400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799
500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266
600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507737 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624
700 -10708.1867253590 -10736.6143955088 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688
800 -10708.1733385055 -10736.0277775931 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693
900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300
1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943
Loop time of 149.449 on 1 procs for 1000 steps with 1440 atoms
Performance: 0.578 ns/day, 41.514 hours/ns, 6.691 timesteps/s
96.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 149.06 | 149.06 | 149.06 | 0.0 | 99.74
Bond | 0.00082946 | 0.00082946 | 0.00082946 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.068351 | 0.068351 | 0.068351 | 0.0 | 0.05
Output | 0.25935 | 0.25935 | 0.25935 | 0.0 | 0.17
Modify | 0.030915 | 0.030915 | 0.030915 | 0.0 | 0.02
Other | | 0.02702 | | | 0.02
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8180 ave 8180 max 8180 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 140400 ave 140400 max 140400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 280800 ave 280800 max 280800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:29

171
examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4 Normal file
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@ -0,0 +1,171 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
720 atoms in group membrane
group adsorbate type 3
720 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2
variable Ecoul equal c_3
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
7 neighbor lists, perpetual/occasional/extra = 6 1 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (6)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) compute group/group, occasional, copy from (7)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(7) neighbor class addition, perpetual, half/full from (6)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -10708.4531746011 -10764.2547791976 55.8016045965 -66.8250335415 -5401.7347845703 -5322.2780762735 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755
100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614
200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321
300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196
400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799
500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266
600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507736 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624
700 -10708.1867253590 -10736.6143955089 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688
800 -10708.1733385055 -10736.0277775930 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693
900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300
1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943
Loop time of 39.6206 on 4 procs for 1000 steps with 1440 atoms
Performance: 2.181 ns/day, 11.006 hours/ns, 25.239 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 34.948 | 37.122 | 39.309 | 31.6 | 93.69
Bond | 0.00046444 | 0.0005914 | 0.00089121 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.20131 | 2.3895 | 4.565 | 124.7 | 6.03
Output | 0.069107 | 0.069157 | 0.069264 | 0.0 | 0.17
Modify | 0.010056 | 0.010403 | 0.010688 | 0.3 | 0.03
Other | | 0.02875 | | | 0.07
Nlocal: 360 ave 380 max 340 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4716 ave 4736 max 4696 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 35100 ave 37050 max 33150 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 70200 ave 74100 max 66300 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:39

0
examples/USER/misc/ilp_gr_hBN/hBN_AB_stack_2L_noH_equi_300K.data → examples/USER/misc/ilp_graphene_hbn/hBN_AB_stack_2L_noH_equi_300K.data
View File

16
examples/USER/misc/ilp_gr_hBN/in.ilp_gr_hBN → examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn
View File

@ -17,10 +17,10 @@ group membrane type 1 2
group adsorbate type 3 4
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ILP/graphene/hBN 16.0 coul/shield 16.0 1
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
pair_coeff * * ILP/graphene/hBN BNCH-old.ILP B N B N # long range
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
@ -48,7 +48,7 @@ fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ILP/graphene/hBN
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable EILP equal c_2
@ -61,12 +61,12 @@ variable Evdw equal c_sldsub
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.15f
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 100000
run 1000

168
examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1 Normal file
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@ -0,0 +1,168 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable EILP equal c_2
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 5 1 0
(1) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (6)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) compute group/group, occasional, copy from (6)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 57.85 | 57.85 | 57.85 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801
100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275
200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807
300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614
400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122
500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319
600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794
700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989
800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553
900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606
1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557
Loop time of 202.063 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.428 ns/day, 56.129 hours/ns, 4.949 timesteps/s
91.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 201.4 | 201.4 | 201.4 | 0.0 | 99.67
Bond | 0.00092697 | 0.00092697 | 0.00092697 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.086005 | 0.086005 | 0.086005 | 0.0 | 0.04
Output | 0.50438 | 0.50438 | 0.50438 | 0.0 | 0.25
Modify | 0.038846 | 0.038846 | 0.038846 | 0.0 | 0.02
Other | | 0.03093 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7840 ave 7840 max 7840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 249628 ave 249628 max 249628 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 253390 ave 253390 max 253390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 253390
Ave neighs/atom = 186.316
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:22

168
examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4 Normal file
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@ -0,0 +1,168 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable EILP equal c_2
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 5 1 0
(1) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (6)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) compute group/group, occasional, copy from (6)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 30.63 | 30.63 | 30.64 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801
100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275
200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807
300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614
400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122
500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319
600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794
700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989
800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553
900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606
1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557
Loop time of 53.3155 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.621 ns/day, 14.810 hours/ns, 18.756 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 49.475 | 50.978 | 52.988 | 18.0 | 95.62
Bond | 0.00045061 | 0.00066602 | 0.00086665 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16491 | 2.1759 | 3.679 | 87.0 | 4.08
Output | 0.11871 | 0.11882 | 0.11911 | 0.0 | 0.22
Modify | 0.012956 | 0.013504 | 0.01387 | 0.3 | 0.03
Other | | 0.02828 | | | 0.05
Nlocal: 340 ave 346 max 336 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 4537.5 ave 4540 max 4534 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 62407 ave 62413 max 62402 min
Histogram: 1 0 0 1 1 0 0 0 0 1
FullNghs: 63347.5 ave 65585 max 61866 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 253926
Ave neighs/atom = 186.71
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:53

6
src/.gitignore vendored
View File

@ -685,6 +685,8 @@
/pair_coul_long.h
/pair_coul_msm.cpp
/pair_coul_msm.h
/pair_coul_shield.cpp
/pair_coul_shield.h
/pair_dipole_cut.cpp
/pair_dipole_cut.h
/pair_dipole_sf.cpp
@ -728,6 +730,10 @@
/pair_hbond_dreiding_lj.h
/pair_hbond_dreiding_morse.cpp
/pair_hbond_dreiding_morse.h
/pair_ilp_graphene_hbn.cpp
/pair_ilp_graphene_hbn.h
/pair_kolmogorov_crespi_full.cpp
/pair_kolmogorov_crespi_full.h
/pair_kolmogorov_crespi_z.cpp
/pair_kolmogorov_crespi_z.h
/pair_lcbop.cpp

56
src/USER-MISC/pair_coul_shield.cpp
View File

@ -29,19 +29,20 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "math_special.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCoulshield::PairCoulshield(LAMMPS *lmp) : Pair(lmp) {
Tapflag = 1;
PairCoulShield::PairCoulShield(LAMMPS *lmp) : Pair(lmp) {
tap_flag = 1;
}
/* ---------------------------------------------------------------------- */
PairCoulshield::~PairCoulshield()
PairCoulShield::~PairCoulShield()
{
if (allocated) {
memory->destroy(setflag);
@ -55,7 +56,7 @@ PairCoulshield::~PairCoulshield()
/* ---------------------------------------------------------------------- */
void PairCoulshield::compute(int eflag, int vflag)
void PairCoulShield::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair,Tap,dTap;
@ -109,13 +110,14 @@ void PairCoulshield::compute(int eflag, int vflag)
r = sqrt(rsq);
r3 = rsq*r;
rarg = 1.0/sigmae[itype][jtype];
th = r3 + pow(rarg,3.0);
th = r3 + MathSpecial::cube(rarg);
epsr = 1.0/pow(th,0.333333333333333333333333);
depsdr = pow(epsr,4.0);
depsdr = MathSpecial::square(epsr);
depsdr *= depsdr;
Vc = qqrd2e*qtmp*q[j]*epsr;
// turn on/off Tapper function
if (Tapflag) {
// turn on/off taper function
if (tap_flag) {
Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
} else {Tap = 1.0; dTap = 0.0;}
@ -134,7 +136,7 @@ void PairCoulshield::compute(int eflag, int vflag)
}
if (eflag) {
if (Tapflag) ecoul = Vc*Tap;
if (tap_flag) ecoul = Vc*Tap;
else ecoul = Vc - offset[itype][jtype];
ecoul *= factor_coul;
}
@ -152,7 +154,7 @@ void PairCoulshield::compute(int eflag, int vflag)
allocate all arrays
------------------------------------------------------------------------- */
void PairCoulshield::allocate()
void PairCoulShield::allocate()
{
allocated = 1;
int n = atom->ntypes;
@ -165,7 +167,6 @@ void PairCoulshield::allocate()
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(sigmae,n+1,n+1,"pair:sigmae");
//memory->create(rme,n+1,n+1,"pair:rme");
memory->create(offset,n+1,n+1,"pair:offset");
}
@ -173,12 +174,12 @@ void PairCoulshield::allocate()
global settings
------------------------------------------------------------------------- */
void PairCoulshield::settings(int narg, char **arg)
void PairCoulShield::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
if (narg == 2) Tapflag = force->numeric(FLERR,arg[1]);
if (narg == 2) tap_flag = force->numeric(FLERR,arg[1]);
// reset cutoffs that have been explicitly set
@ -194,7 +195,7 @@ void PairCoulshield::settings(int narg, char **arg)
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCoulshield::coeff(int narg, char **arg)
void PairCoulShield::coeff(int narg, char **arg)
{
if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@ -226,7 +227,7 @@ void PairCoulshield::coeff(int narg, char **arg)
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulshield::init_style()
void PairCoulShield::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/shield requires atom attribute q");
@ -238,7 +239,7 @@ void PairCoulshield::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairCoulshield::init_one(int i, int j)
double PairCoulShield::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
error->all(FLERR,"for pair style coul/shield, parameters need to be set explicitly for all pairs.");
@ -252,7 +253,7 @@ double PairCoulshield::init_one(int i, int j)
r = cut[i][j];
r3 = r*r*r;
rarg = 1.0/sigmae[i][j];
th = r3 + pow(rarg,3.0);
th = r3 + MathSpecial::cube(rarg);
epsr = 1.0/pow(th,0.333333333333333333);
offset[i][j] = qqrd2e*q[i]*q[j]*epsr;
} else offset[i][j] = 0.0;
@ -269,7 +270,7 @@ double PairCoulshield::init_one(int i, int j)
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulshield::write_restart(FILE *fp)
void PairCoulShield::write_restart(FILE *fp)
{
write_restart_settings(fp);
@ -288,7 +289,7 @@ void PairCoulshield::write_restart(FILE *fp)
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulshield::read_restart(FILE *fp)
void PairCoulShield::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
@ -312,7 +313,7 @@ void PairCoulshield::read_restart(FILE *fp)
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulshield::write_restart_settings(FILE *fp)
void PairCoulShield::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
@ -323,7 +324,7 @@ void PairCoulshield::write_restart_settings(FILE *fp)
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulshield::read_restart_settings(FILE *fp)
void PairCoulShield::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
@ -337,7 +338,7 @@ void PairCoulshield::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulshield::single(int i, int j, int itype, int jtype,
double PairCoulShield::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
@ -349,13 +350,14 @@ double PairCoulshield::single(int i, int j, int itype, int jtype,
r = sqrt(rsq);
r3 = rsq*r;
rarg = 1.0/sigmae[itype][jtype];
th = r3 + pow(rarg,3.0);
th = r3 + MathSpecial::cube(rarg);
epsr = 1.0/pow(th,0.333333333333333333);
depsdr = pow(epsr,4.0);
depsdr = epsr*epsr;
depsdr *= depsdr;
Vc = qqrd2e*q[i]*q[j]*epsr;
// turn on/off Tapper function
if (Tapflag) {
// turn on/off taper function
if (tap_flag) {
Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
} else {Tap = 1.0; dTap = 0.0;}
@ -364,7 +366,7 @@ double PairCoulshield::single(int i, int j, int itype, int jtype,
fvc = forcecoul*Tap - Vc*dTap/r;
fforce = factor_coul*fvc;
if (Tapflag) phishieldec = factor_coul*Vc*Tap;
if (tap_flag) phishieldec = factor_coul*Vc*Tap;
else phishieldec = Vc - offset[itype][jtype];
return factor_coul*phishieldec;
}

10
src/USER-MISC/pair_coul_shield.h
View File

@ -13,7 +13,7 @@
#ifdef PAIR_CLASS
PairStyle(coul/shield,PairCoulshield)
PairStyle(coul/shield,PairCoulShield)
#else
@ -24,10 +24,10 @@ PairStyle(coul/shield,PairCoulshield)
namespace LAMMPS_NS {
class PairCoulshield : public Pair {
class PairCoulShield : public Pair {
public:
PairCoulshield(class LAMMPS *);
virtual ~PairCoulshield();
PairCoulShield(class LAMMPS *);
virtual ~PairCoulShield();
virtual void compute(int, int);
@ -47,7 +47,7 @@ class PairCoulshield : public Pair {
double **cut;
double **sigmae, **offset;
//double a_eps, b_eps, eps_s;
int Tapflag;
int tap_flag;
void allocate();

54
src/USER-MISC/pair_ilp_gr_hBN.cpp → src/USER-MISC/pair_ilp_graphene_hbn.cpp
View File

@ -20,12 +20,12 @@
[Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <mpi.h>
#include "pair_ilp_gr_hBN.h"
#include "pair_ilp_graphene_hbn.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
@ -44,9 +44,10 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairILP::PairILP(LAMMPS *lmp) : Pair(lmp)
PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
restartinfo = 0;
// initialize element to parameter maps
nelements = 0;
@ -78,7 +79,7 @@ PairILP::PairILP(LAMMPS *lmp) : Pair(lmp)
/* ---------------------------------------------------------------------- */
PairILP::~PairILP()
PairILPGrapheneHBN::~PairILPGrapheneHBN()
{
memory->destroy(ILP_numneigh);
memory->sfree(ILP_firstneigh);
@ -105,9 +106,9 @@ PairILP::~PairILP()
/* ---------------------------------------------------------------------- */
void PairILP::compute(int eflag, int vflag)
void PairILPGrapheneHBN::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,id,k,l,kk,ll;
int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
tagint itag,jtag;
double prodnorm1,prodnorm2,fkcx,fkcy,fkcz;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2;
@ -188,7 +189,7 @@ void PairILP::compute(int eflag, int vflag)
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r8inv = r6inv*r2inv;
// turn on/off Tapper function
// turn on/off taper function
if (tap_flag) {
Rcut = sqrt(cutsq[itype][jtype]);
Tap = calc_Tap(r,Rcut);
@ -302,21 +303,16 @@ void PairILP::compute(int eflag, int vflag)
/* ----------------------------------------------------------------------
Calculate the normals for each atom
------------------------------------------------------------------------- */
void PairILP::calc_normal()
void PairILPGrapheneHBN::calc_normal()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int cont,k,kk,cont1,id,ip,m;
tagint itag,jtag;
double dist,nn,xtp,ytp,ztp,delx,dely,delz,nn2;
int i,j,ii,jj,inum,jnum;
int cont,id,ip,m;
double nn,xtp,ytp,ztp,delx,dely,delz,nn2;
int *ilist,*jlist;
double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3];
double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3];
double **x = atom->x;
int *type = atom->type;
int ntypes = atom->ntypes;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
// grow normal array if necessary
@ -338,7 +334,6 @@ void PairILP::calc_normal()
xtp = x[i][0];
ytp = x[i][1];
ztp = x[i][2];
itype = type[i];
// Initialize the arrays
for (id = 0; id < 3; id++){
@ -638,7 +633,7 @@ void PairILP::calc_normal()
init specific to this pair style
------------------------------------------------------------------------- */
void PairILP::init_style()
void PairILPGrapheneHBN::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR,"Pair style ILP requires newton pair on");
@ -678,9 +673,9 @@ void PairILP::init_style()
ILP_pair_numneigh for calculating force
------------------------------------------------------------------------- */
void PairILP::ILP_neigh()
void PairILPGrapheneHBN::ILP_neigh()
{
int i,j,ii,jj,n,np,allnum,inum,jnum,itype,jtype;
int i,j,ii,jj,n,allnum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int *neighptr;
@ -696,7 +691,6 @@ void PairILP::ILP_neigh()
ILP_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),"ILP:firstneigh");
}
inum = list->inum;
allnum = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
@ -747,7 +741,7 @@ void PairILP::ILP_neigh()
allocate all arrays
------------------------------------------------------------------------- */
void PairILP::allocate()
void PairILPGrapheneHBN::allocate()
{
allocated = 1;
int n = atom->ntypes;
@ -767,7 +761,7 @@ void PairILP::allocate()
global settings
------------------------------------------------------------------------- */
void PairILP::settings(int narg, char **arg)
void PairILPGrapheneHBN::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");
if (strcmp(force->pair_style,"hybrid/overlay")!=0)
@ -790,7 +784,7 @@ void PairILP::settings(int narg, char **arg)
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairILP::coeff(int narg, char **arg)
void PairILPGrapheneHBN::coeff(int narg, char **arg)
{
int i,j,n;
@ -853,7 +847,7 @@ void PairILP::coeff(int narg, char **arg)
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairILP::init_one(int i, int j)
double PairILPGrapheneHBN::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
@ -871,7 +865,7 @@ double PairILP::init_one(int i, int j)
read Interlayer potential file
------------------------------------------------------------------------- */
void PairILP::read_file(char *filename)
void PairILPGrapheneHBN::read_file(char *filename)
{
int params_per_line = 13;
char **words = new char*[params_per_line+1];
@ -1016,7 +1010,7 @@ void PairILP::read_file(char *filename)
/* ---------------------------------------------------------------------- */
double PairILP::single(int i, int j, int itype, int jtype, double rsq,
double PairILPGrapheneHBN::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
@ -1027,7 +1021,7 @@ double PairILP::single(int i, int j, int itype, int jtype, double rsq,
Param& p = params[iparam_ij];
r = sqrt(rsq);
// turn on/off Tapper function
// turn on/off taper function
if (tap_flag) {
Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
@ -1052,7 +1046,7 @@ double PairILP::single(int i, int j, int itype, int jtype, double rsq,
/* ---------------------------------------------------------------------- */
int PairILP::pack_forward_comm(int n, int *list, double *buf,
int PairILPGrapheneHBN::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m,id,ip,l;
@ -1085,7 +1079,7 @@ int PairILP::pack_forward_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
void PairILP::unpack_forward_comm(int n, int first, double *buf)
void PairILPGrapheneHBN::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last,id,ip,l;

14
src/USER-MISC/pair_ilp_gr_hBN.h → src/USER-MISC/pair_ilp_graphene_hbn.h
View File

@ -13,12 +13,12 @@
#ifdef PAIR_CLASS
PairStyle(ILP/graphene/hBN,PairILP)
PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN)
#else
#ifndef LMP_PAIR_ILP_H
#define LMP_PAIR_ILP_H
#ifndef LMP_PAIR_ILP_GRAPHENE_HBN_H
#define LMP_PAIR_ILP_GRAPHENE_HBN_H
#include "pair.h"
#include "my_page.h"
@ -26,10 +26,10 @@ PairStyle(ILP/graphene/hBN,PairILP)
namespace LAMMPS_NS {
class PairILP : public Pair {
class PairILPGrapheneHBN : public Pair {
public:
PairILP(class LAMMPS *);
virtual ~PairILP();
PairILPGrapheneHBN(class LAMMPS *);
virtual ~PairILPGrapheneHBN();
virtual void compute(int, int);
void settings(int, char **);
@ -49,7 +49,7 @@ class PairILP : public Pair {
MyPage<int> *ipage; // neighbor list pages
int *ILP_numneigh; // # of pair neighbors for each atom
int **ILP_firstneigh; // ptr to 1st neighbor of each atom
int tap_flag; // flag to turn on/off Tapper function
int tap_flag; // flag to turn on/off taper function
struct Param {
double z0,alpha,epsilon,C,delta,d,sR,reff,C6,S;

23
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
View File

@ -107,7 +107,7 @@ PairKolmogorovCrespiFull::~PairKolmogorovCrespiFull()
void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,id,k,l,kk,ll;
int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
tagint itag,jtag;
double prodnorm1,prodnorm2,fkcx,fkcy,fkcz;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2;
@ -188,7 +188,7 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r8inv = r2inv*r6inv;
// turn on/off Tapper function
// turn on/off taper function
if (tap_flag) {
Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
@ -305,19 +305,14 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
------------------------------------------------------------------------- */
void PairKolmogorovCrespiFull::calc_normal()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int cont,k,kk,cont1,id,ip,m;
tagint itag,jtag;
double dist,nn,xtp,ytp,ztp,delx,dely,delz,nn2;
int i,j,ii,jj,inum,jnum;
int cont,id,ip,m;
double nn,xtp,ytp,ztp,delx,dely,delz,nn2;
int *ilist,*jlist;
double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3];
double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3];
double **x = atom->x;
int *type = atom->type;
int ntypes = atom->ntypes;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
// grow normal array if necessary
@ -339,7 +334,6 @@ void PairKolmogorovCrespiFull::calc_normal()
xtp = x[i][0];
ytp = x[i][1];
ztp = x[i][2];
itype = type[i];
// Initialize the arrays
for (id = 0; id < 3; id++){
@ -685,8 +679,8 @@ void PairKolmogorovCrespiFull::init_style()
void PairKolmogorovCrespiFull::KC_neigh()
{
int i,j,ii,jj,n,np,allnum,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,dS;
int i,j,ii,jj,n,allnum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int *neighptr;
@ -702,7 +696,6 @@ void PairKolmogorovCrespiFull::KC_neigh()
"KolmogorovCrespiFull:firstneigh");
}
inum = list->inum;
allnum = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
@ -1033,7 +1026,7 @@ double PairKolmogorovCrespiFull::single(int i, int j, int itype, int jtype, doub
Param& p = params[iparam_ij];
r = sqrt(rsq);
// turn on/off Tapper function
// turn on/off taper function
if (tap_flag) {
Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));

2
src/USER-MISC/pair_kolmogorov_crespi_full.h
View File

@ -49,7 +49,7 @@ class PairKolmogorovCrespiFull : public Pair {
MyPage<int> *ipage; // neighbor list pages
int *KC_numneigh; // # of pair neighbors for each atom
int **KC_firstneigh; // ptr to 1st neighbor of each atom
int tap_flag; // flag to turn on/off Tapper function
int tap_flag; // flag to turn on/off taper function
struct Param {