update examples to standard lammps conventions
This commit is contained in:
Colin Denniston
@ -1,102 +0,0 @@
|
||||
# Fix print output for fix printCM
|
||||
0 0 0 -5.00000000070583e-08 0 0 0
|
||||
100 0.000862030487945766 0.0123054296765635 0.0122731465590126 0.0388471409686686 0.554171814767862 0.549353841801444
|
||||
200 0.00185887929142589 0.026504860571345 0.0263575026345381 0.0406164349263177 0.577485522778581 0.572358123657981
|
||||
300 0.00288609111410669 0.041071186430552 0.0407387949853162 0.0414733855376221 0.586334796005238 0.579029199408148
|
||||
400 0.00392999369142328 0.0557729852014459 0.0552309274319543 0.0420073620501712 0.589116414842769 0.579447580483091
|
||||
500 0.00498536275941171 0.070499164057003 0.0697415367523594 0.0424046217549586 0.588483528276922 0.579713082803989
|
||||
600 0.00604958471579167 0.0851758456067289 0.0842109166632151 0.0427225597696811 0.585256835192702 0.578675424528672
|
||||
700 0.00712105404933591 0.0997436526892664 0.0986256150648839 0.0429880258004064 0.579826819459789 0.574965309339321
|
||||
800 0.00819868650413988 0.114150894221279 0.112970143937093 0.0432171820009732 0.572436469824202 0.571379696846873
|
||||
900 0.00928167490285266 0.128350199155429 0.127214300017093 0.0434177041449832 0.563212233113465 0.568141900579381
|
||||
1000 0.0103693800467608 0.142297070506134 0.141346756412092 0.0435952275760965 0.552255756217314 0.563198941286352
|
||||
1100 0.0114612757740303 0.155949207303663 0.155363270006244 0.0437534628364653 0.539645345817638 0.557547826275249
|
||||
1200 0.0125569146112762 0.16926611615961 0.169243664446122 0.0438950800605928 0.525448494610828 0.552385484155222
|
||||
1300 0.0136559090539262 0.182208942626165 0.182971608380899 0.0440222186903751 0.509729009151129 0.546362371549647
|
||||
1400 0.0147579190343771 0.194740388291494 0.196542287352516 0.0441365813451693 0.49254820772961 0.53923843292572
|
||||
1500 0.0158626435855424 0.206824684659766 0.20994260685037 0.0442396069433182 0.473967311999804 0.532221947561911
|
||||
1600 0.016969815144629 0.218427601281069 0.223154967935698 0.0443325350264529 0.454048234578232 0.52490993166384
|
||||
1700 0.0180791952377331 0.229516470517873 0.23617097657798 0.0444164592397298 0.432854159986641 0.516564181615295
|
||||
1800 0.0191905712013339 0.240060223538286 0.248981532998294 0.044492359500651 0.41044987377188 0.507890446812699
|
||||
1900 0.0203037536403243 0.250029432395321 0.261570985506027 0.0445611192532371 0.386901867661691 0.499132572020635
|
||||
2000 0.0214185743448717 0.259396354393085 0.27392793783106 0.0446235485425134 0.36227844753556 0.489625430842279
|
||||
2100 0.0225348845239784 0.268134976647594 0.286044452302522 0.0446803959508529 0.33664970767355 0.479528537282853
|
||||
2200 0.0236525533438346 0.276221059771718 0.297907925422812 0.0447323522651497 0.310087425177735 0.469306149162182
|
||||
2300 0.0247714666787315 0.283632179279284 0.309505839706109 0.0447800603260404 0.282664970647061 0.458617441651712
|
||||
2400 0.0258915259587789 0.290347763502706 0.320829824034913 0.0448241232027665 0.254457178820598 0.44728722136532
|
||||
2500 0.0270126471290237 0.29634912772668 0.331869872099864 0.0448651027638521 0.225540156619441 0.435694872117013
|
||||
2600 0.0281347597089685 0.30161950408948 0.34261406670463 0.0449035206640385 0.195991101443378 0.423810112638771
|
||||
2700 0.0292578058434875 0.306144066595306 0.353053315437221 0.0449398633594251 0.165888127664992 0.41137110526867
|
||||
2800 0.030381739316435 0.309909951263501 0.363179201634917 0.0449745786568748 0.135310062250947 0.398557628586131
|
||||
2900 0.0315065245470535 0.312906271705092 0.372981337255243 0.0450080686588849 0.104336253816866 0.385510764564962
|
||||
3000 0.0326321354733442 0.315124130290068 0.38245041225465 0.0450406882166782 0.0730464235910661 0.372042169913947
|
||||
3100 0.0337585542236816 0.316556625622056 0.391578764333674 0.0450727382300617 0.0415205367630292 0.358160568106331
|
||||
3200 0.034885766256052 0.31719885875625 0.400357663441649 0.0451036547071826 0.00983907573551093 0.344030677469557
|
||||
3300 0.0360136872580489 0.317048008823491 0.408777748573793 0.045129040578256 -0.0219107556190337 0.32955676892105
|
||||
3400 0.0371421729145326 0.316103516604794 0.416830876205518 0.0451489780670191 -0.0536371623936908 0.314668838998143
|
||||
3500 0.0382710977786635 0.314367093900902 0.424509118504444 0.0451643056938233 -0.0852504239010061 0.299493529440764
|
||||
3600 0.039400355723286 0.311842668099774 0.431804221276515 0.0451757343394363 -0.116662994488708 0.284066192756869
|
||||
3700 0.0405298571235071 0.308536328771854 0.438709086698874 0.0451838769711716 -0.147789438945399 0.268314898256792
|
||||
3800 0.0416595266582488 0.304456275109671 0.445217419249879 0.0451892685671837 -0.178546427643007 0.252292051488811
|
||||
3900 0.0427893015653343 0.299612762874147 0.451322687530176 0.0451923807983904 -0.208852773056517 0.236070778082722
|
||||
4000 0.0439191302054448 0.294018050086672 0.457018894174797 0.0451936331558271 -0.238629493808845 0.219614191498541
|
||||
4100 0.0450489708508549 0.287686340949681 0.462300983177224 0.0451934002599296 -0.267799890966025 0.202923522400675
|
||||
4200 0.0461787906402368 0.280633727679951 0.46716400466032 0.0451920174774752 -0.296289636112744 0.186067111728447
|
||||
4300 0.0473085646518621 0.272878130115369 0.471603197062402 0.0451897853348954 -0.324026864816915 0.169048732639397
|
||||
4400 0.0484382750721604 0.264439232972262 0.475614593651548 0.0451869725702152 -0.350942268020778 0.151851130542203
|
||||
4500 0.049567910442748 0.255338420725821 0.479194641553675 0.045183819044704 -0.37696918707268 0.134518378555459
|
||||
4600 0.0506974649686312 0.245598710206154 0.482339905708537 0.0451805383879157 -0.402043707551555 0.117079995982193
|
||||
4700 0.0518269378826076 0.235244680971009 0.485047513161603 0.0451773197428711 -0.426104742058066 0.0995240797086898
|
||||
4800 0.052956332860714 0.224302403572179 0.487315158338437 0.0451743295087643 -0.449094108942282 0.0818709366680246
|
||||
4900 0.0540856574759206 0.212799365966729 0.489140744652625 0.0451717131537436 -0.470956607153122 0.0641572680070745
|
||||
5000 0.0552149226836002 0.200764398290593 0.490522557427433 0.0451695961979473 -0.491640075621893 0.04638589199498
|
||||
5100 0.0563441423344801 0.188227596194827 0.491459457220784 0.045168084821581 -0.511095441430305 0.0285636095658589
|
||||
5200 0.057473332702688 0.17522024305006 0.491950642641828 0.0451672665812737 -0.529276763383753 0.0107219134977892
|
||||
5300 0.0586025120187606 0.161774731300966 0.491995614110831 0.0451672105484937 -0.546141262620913 -0.00712340874154904
|
||||
5400 0.0597317000030321 0.147924483163387 0.491594377124997 0.0451679668568151 -0.561649340260399 -0.0249682994538472
|
||||
5500 0.0608609173904777 0.133703870891375 0.490747365943808 0.0451695662898269 -0.575764591653344 -0.0427904594790811
|
||||
5600 0.0619901854374394 0.119148136830319 0.489455318876335 0.045172019632285 -0.58845381491908 -0.0605675872373609
|
||||
5700 0.0631195254064262 0.104293313359254 0.487719399569343 0.0451753165168183 -0.599687010953726 -0.0782918862578729
|
||||
5800 0.0642489580246837 0.0891761427946867 0.48554123315084 0.0451794242166182 -0.609437382803975 -0.0959482954276833
|
||||
5900 0.0653785029101205 0.0738339973249388 0.482922791336815 0.0451842864271072 -0.617681336848454 -0.113513947143333
|
||||
6000 0.066508177961606 0.0583047989558168 0.479866421958322 0.0451898217427784 -0.624398482710512 -0.13097562667804
|
||||
6100 0.0676379987117821 0.0426269393910158 0.476374926355184 0.0451959219945778 -0.629571635891283 -0.148321352569801
|
||||
6200 0.0687679776380947 0.0268391997711945 0.472451499697091 0.0452024505874852 -0.633186826926119 -0.165530745880477
|
||||
6300 0.0698981234280855 0.010980670154477 0.468099704053854 0.0452092406152506 -0.635233314989177 -0.182586480506518
|
||||
6400 0.0710284401951811 -0.00490933141996686 0.463323535196445 0.0452160926978174 -0.6357036064805 -0.199476058698813
|
||||
6500 0.0721589266379823 -0.0207913404308021 0.45812741824118 0.0452227725683118 -0.634593480754686 -0.216181770202423
|
||||
6600 0.0732895751329617 -0.0366258280722564 0.4525161672434 0.0452290081924521 -0.631902021250181 -0.232684251091254
|
||||
6700 0.0744203707468311 -0.0523732842796794 0.446495021852624 0.0452344861625994 -0.627631650070581 -0.248968525167056
|
||||
6800 0.0755512901476198 -0.0679943016610313 0.440069676657587 0.0452388471144838 -0.621788164979803 -0.265018013055149
|
||||
6900 0.0766823003834517 -0.0834496603398142 0.433246256793092 0.0452416796548797 -0.614380775066988 -0.280812614225028
|
||||
7000 0.0778133574838834 -0.0987004136215648 0.426031330764786 0.0452425120772539 -0.605422129824962 -0.296334220434174
|
||||
7100 0.0789444048161975 -0.113707974241796 0.418431952538327 0.0452408008213928 -0.594928335060022 -0.311565205779314
|
||||
7200 0.0800753710948757 -0.128434200729008 0.410455666617559 0.0452359139442821 -0.582918944331306 -0.326484492981048
|
||||
7300 0.0812061678888613 -0.142841483083547 0.402110518367413 0.0452271068609726 -0.56941690886808 -0.34107027310023
|
||||
7400 0.0823366868879886 -0.156892832550369 0.393405100664375 0.0452137152253101 -0.554451229049732 -0.355302873244928
|
||||
7500 0.0834668517149059 -0.170552623647645 0.384348175871066 0.0451996568242026 -0.538109504133949 -0.3691955162588
|
||||
7600 0.0845966786525954 -0.183787343990598 0.374948167603608 0.0451866668285694 -0.520452068779317 -0.38274791022926
|
||||
7700 0.0857261928989984 -0.196564598620189 0.365213708220604 0.0451746173490727 -0.501519185936364 -0.395949104997471
|
||||
7800 0.0868554160875386 -0.208853033947754 0.355153722643092 0.0451633558994798 -0.481353961460688 -0.408788219630066
|
||||
7900 0.0879843659433281 -0.220622412047369 0.344777414582154 0.0451527246802332 -0.460002566524482 -0.421253498591182
|
||||
8000 0.0891130563099555 -0.23184368872928 0.334094257673578 0.0451425726521896 -0.437514339207557 -0.433334064382642
|
||||
8100 0.0902414974316455 -0.2424890932098 0.323113996077294 0.0451327640586105 -0.413941813252733 -0.445019966270824
|
||||
8200 0.0913696964100858 -0.252532207710901 0.311846632415356 0.0451231839591836 -0.389340685397376 -0.456300911536802
|
||||
8300 0.0924976577671853 -0.261948045581448 0.300302411401681 0.0451137412199365 -0.363769731247534 -0.467166979522632
|
||||
8400 0.0936253840550899 -0.270713126771119 0.288491813206727 0.0451043693754287 -0.337290679181815 -0.477609349083408
|
||||
8500 0.0947528764650488 -0.278805549717671 0.27642554360983 0.0450950257530967 -0.309968050973641 -0.487619421164766
|
||||
8600 0.0958801353970909 -0.286205058917463 0.264114517046721 0.0450856892760242 -0.281868977005235 -0.497188713267531
|
||||
8700 0.0970071609627085 -0.292893107630846 0.251569845366989 0.0450763573660472 -0.253062992836497 -0.506309612902325
|
||||
8800 0.0981339534030675 -0.298852915325574 0.238802829407755 0.0450670423558943 -0.223621822504895 -0.514975070718216
|
||||
8900 0.0992605134153133 -0.304069519580759 0.22582494504124 0.0450577677864475 -0.193619152641678 -0.523178137637988
|
||||
9000 0.100386842388707 -0.308529822260866 0.212647830382011 0.0450485649429167 -0.163130400331202 -0.530912414901356
|
||||
9100 0.101512942559987 -0.312222629827916 0.199283277442076 0.0450394698977844 -0.13223247655603 -0.538172167586218
|
||||
9200 0.102638817103052 -0.315138687696582 0.185743221236983 0.0450305212343208 -0.10100354632644 -0.544951888794609
|
||||
9300 0.103764470171021 -0.317270708558709 0.172039727157391 0.0450217585121602 -0.0695227861974757 -0.551246411933543
|
||||
9400 0.104889906908796 -0.318613394619428 0.158184981612494 0.0450132214234404 -0.0378701397929889 -0.557051185837414
|
||||
9500 0.106015133451531 -0.319163453704509 0.144191282694294 0.0450049494770458 -0.00612607214576512 -0.562362036167608
|
||||
9600 0.107140156919558 -0.318919609223059 0.130071028527096 0.0449969819880669 0.0256286759940099 -0.567175055659959
|
||||
9700 0.108264985414172 -0.317882604002936 0.115836707124747 0.0449893581153677 0.0573133323763313 -0.571486831413926
|
||||
9800 0.109389628012451 -0.316055198056751 0.101500887824999 0.0449821167122573 0.0888473342969765 -0.575294393321441
|
||||
9900 0.110514094754186 -0.313442160379143 0.0870762114315177 0.0449752958236126 0.120150564786057 -0.578595028443573
|
||||
10000 0.111638396610866 -0.310050254915132 0.0725753806410134 0.0449689317481374 0.151143582530835 -0.581386376944959
|
||||
@ -4,9 +4,10 @@
|
||||
# Run consists of a colloidal particle being dragged with a constant force #
|
||||
# through an LB-fluid. The colloidal particle could be single atom or #
|
||||
# be a composite particle. Composite particles could be bonded or just #
|
||||
# rigidly constrained to stay together. #
|
||||
# rigidly constrained to stay together. You can set flags in the script to #
|
||||
# change these. #
|
||||
# #
|
||||
# Sample output from this run can be found in the files with ".log" #
|
||||
# Sample output from this run can be found in the files with "log." #
|
||||
# located in the same directory. #
|
||||
#===========================================================================#
|
||||
|
||||
@ -133,7 +134,7 @@ if "${is_bonded} == 1" then &
|
||||
else &
|
||||
"variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
|
||||
|
||||
fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
#run 100000
|
||||
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.1
Normal file
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.1
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# single particle drag tests #
|
||||
# #
|
||||
# Run consists of a colloidal particle being dragged with a constant force #
|
||||
# through an LB-fluid. The colloidal particle could be single atom or #
|
||||
# be a composite particle. Composite particles could be bonded or just #
|
||||
# rigidly constrained to stay together. You can set flags in the script to #
|
||||
# change these. #
|
||||
# #
|
||||
# Sample output from this run can be found in the files with "log." #
|
||||
# located in the same directory. #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style molecular
|
||||
|
||||
region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Set up particles with n_nodes and decide if bonded or rigid
|
||||
#----------------------------------------------------------------------------
|
||||
variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
|
||||
variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
|
||||
# bond parameters set for n_node = 4 case)
|
||||
variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
|
||||
|
||||
variable tstep equal 0.00025
|
||||
|
||||
if "${is_bonded} == 1" then "create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" else "create_box 1 mydomain"
|
||||
create_box 1 mydomain
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
if "${n_nodes} == 1" then "create_atoms 1 single 0.0 0.0 0.0" elif "${n_nodes} == 4" "create_atoms 1 single 0.0 0.0 0.204124" "create_atoms 1 single -0.096225 -0.166667 -0.0680414" "create_atoms 1 single -0.096225 0.166667 -0.0680414" "create_atoms 1 single 0.19245 0. -0.0680414" elif "${n_nodes} == 6" "create_atoms 1 single 0.204124 0.0000000 0.0000000" "create_atoms 1 single -0.204124 0.0000000 0.0000000" "create_atoms 1 single 0.0000000 0.204124 0.0000000" "create_atoms 1 single 0.0000000 -0.204124 0.0000000" "create_atoms 1 single 0.0000000 0.0000000 0.204124" "create_atoms 1 single 0.0000000 0.0000000 -0.204124"
|
||||
create_atoms 1 single 0.0 0.0 0.204124
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 1 single -0.096225 -0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 1 single -0.096225 0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 single 0.19245 0. -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interactions between particles & create bonds
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 5.88
|
||||
pair_coeff * * 0.0 0.0 5.88
|
||||
|
||||
variable total_mass equal 0.002398 # particle mass
|
||||
variable node_mass equal "v_total_mass / v_n_nodes"
|
||||
mass * ${node_mass}
|
||||
mass * 0.0005995
|
||||
|
||||
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 1.0 0.333333333" "create_bonds many all all 1 0.3 0.35"
|
||||
|
||||
#velocity all set 0.02 0.0 0.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
|
||||
# to drag particles through the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
variable total_force equal 1.0 # total external force on the particle
|
||||
variable node_force equal "v_total_force / v_n_nodes"
|
||||
variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
|
||||
fix drag all addforce 0.25 v_oscillateY v_oscillateZ
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particle (group all here)
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix).
|
||||
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
|
||||
# lattice spacing dx=1.2.
|
||||
# Different ".log" files in this directory show the output with the stencil
|
||||
# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
|
||||
#----------------------------------------------------------------------------
|
||||
timestep ${tstep}
|
||||
timestep 0.00025
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 3 dx 1.2
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
#dumpxdmf 1000 fflow
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object or an elastically bonded object
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
|
||||
if "${n_nodes} == 1 || ${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
|
||||
fix 3 all rigid group 1 all
|
||||
1 rigid bodies with 4 atoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables containing the positions/velocity of the colloids center
|
||||
# of mass.
|
||||
#----------------------------------------------------------------------------
|
||||
variable cmx equal xcm(all,x)
|
||||
variable cmy equal xcm(all,y)
|
||||
variable cmz equal xcm(all,z)
|
||||
|
||||
variable vcmx equal vcm(all,x)
|
||||
variable vcmy equal vcm(all,y)
|
||||
variable vcmz equal vcm(all,z)
|
||||
|
||||
if "${is_bonded} == 1" then "variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
|
||||
variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt0.00025.out
|
||||
|
||||
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 2.1529156e-12
|
||||
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
|
||||
Loop time of 185.434 on 1 procs for 10000 steps with 4 atoms
|
||||
|
||||
Performance: 1164.837 ns/day, 0.021 hours/ns, 53.928 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.02024 | 0.02024 | 0.02024 | 0.0 | 0.01
|
||||
Bond | 0.0011585 | 0.0011585 | 0.0011585 | 0.0 | 0.00
|
||||
Neigh | 8.88e-05 | 8.88e-05 | 8.88e-05 | 0.0 | 0.00
|
||||
Comm | 0.011615 | 0.011615 | 0.011615 | 0.0 | 0.01
|
||||
Output | 8.32e-05 | 8.32e-05 | 8.32e-05 | 0.0 | 0.00
|
||||
Modify | 185.36 | 185.36 | 185.36 | 0.0 | 99.96
|
||||
Other | | 0.04469 | | | 0.02
|
||||
|
||||
Nlocal: 4 ave 4 max 4 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 6
|
||||
Ave neighs/atom = 1.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
#run 100000
|
||||
|
||||
Total wall time: 0:03:05
|
||||
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.4
Normal file
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.4
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# single particle drag tests #
|
||||
# #
|
||||
# Run consists of a colloidal particle being dragged with a constant force #
|
||||
# through an LB-fluid. The colloidal particle could be single atom or #
|
||||
# be a composite particle. Composite particles could be bonded or just #
|
||||
# rigidly constrained to stay together. You can set flags in the script to #
|
||||
# change these. #
|
||||
# #
|
||||
# Sample output from this run can be found in the files with "log." #
|
||||
# located in the same directory. #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style molecular
|
||||
|
||||
region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Set up particles with n_nodes and decide if bonded or rigid
|
||||
#----------------------------------------------------------------------------
|
||||
variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
|
||||
variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
|
||||
# bond parameters set for n_node = 4 case)
|
||||
variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
|
||||
|
||||
variable tstep equal 0.00025
|
||||
|
||||
if "${is_bonded} == 1" then "create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" else "create_box 1 mydomain"
|
||||
create_box 1 mydomain
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
if "${n_nodes} == 1" then "create_atoms 1 single 0.0 0.0 0.0" elif "${n_nodes} == 4" "create_atoms 1 single 0.0 0.0 0.204124" "create_atoms 1 single -0.096225 -0.166667 -0.0680414" "create_atoms 1 single -0.096225 0.166667 -0.0680414" "create_atoms 1 single 0.19245 0. -0.0680414" elif "${n_nodes} == 6" "create_atoms 1 single 0.204124 0.0000000 0.0000000" "create_atoms 1 single -0.204124 0.0000000 0.0000000" "create_atoms 1 single 0.0000000 0.204124 0.0000000" "create_atoms 1 single 0.0000000 -0.204124 0.0000000" "create_atoms 1 single 0.0000000 0.0000000 0.204124" "create_atoms 1 single 0.0000000 0.0000000 -0.204124"
|
||||
create_atoms 1 single 0.0 0.0 0.204124
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 1 single -0.096225 -0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 single -0.096225 0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 single 0.19245 0. -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interactions between particles & create bonds
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 5.88
|
||||
pair_coeff * * 0.0 0.0 5.88
|
||||
|
||||
variable total_mass equal 0.002398 # particle mass
|
||||
variable node_mass equal "v_total_mass / v_n_nodes"
|
||||
mass * ${node_mass}
|
||||
mass * 0.0005995
|
||||
|
||||
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 1.0 0.333333333" "create_bonds many all all 1 0.3 0.35"
|
||||
|
||||
#velocity all set 0.02 0.0 0.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
|
||||
# to drag particles through the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
variable total_force equal 1.0 # total external force on the particle
|
||||
variable node_force equal "v_total_force / v_n_nodes"
|
||||
variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
|
||||
fix drag all addforce 0.25 v_oscillateY v_oscillateZ
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particle (group all here)
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix).
|
||||
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
|
||||
# lattice spacing dx=1.2.
|
||||
# Different ".log" files in this directory show the output with the stencil
|
||||
# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
|
||||
#----------------------------------------------------------------------------
|
||||
timestep ${tstep}
|
||||
timestep 0.00025
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 3 dx 1.2
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
#dumpxdmf 1000 fflow
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object or an elastically bonded object
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
|
||||
if "${n_nodes} == 1 || ${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
|
||||
fix 3 all rigid group 1 all
|
||||
1 rigid bodies with 4 atoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables containing the positions/velocity of the colloids center
|
||||
# of mass.
|
||||
#----------------------------------------------------------------------------
|
||||
variable cmx equal xcm(all,x)
|
||||
variable cmy equal xcm(all,y)
|
||||
variable cmz equal xcm(all,z)
|
||||
|
||||
variable vcmx equal vcm(all,x)
|
||||
variable vcmy equal vcm(all,y)
|
||||
variable vcmz equal vcm(all,z)
|
||||
|
||||
if "${is_bonded} == 1" then "variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
|
||||
variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt0.00025.out
|
||||
|
||||
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.763 | 6.857 | 7.138 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 2.1529156e-12
|
||||
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
|
||||
Loop time of 154.466 on 4 procs for 10000 steps with 4 atoms
|
||||
|
||||
Performance: 1398.367 ns/day, 0.017 hours/ns, 64.739 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.013169 | 0.01792 | 0.021577 | 2.3 | 0.01
|
||||
Bond | 0.0019565 | 0.0021447 | 0.0023408 | 0.4 | 0.00
|
||||
Neigh | 7.55e-05 | 9.69e-05 | 0.0001173 | 0.0 | 0.00
|
||||
Comm | 0.07056 | 0.076818 | 0.084499 | 2.1 | 0.05
|
||||
Output | 2.85e-05 | 4.4925e-05 | 9.24e-05 | 0.0 | 0.00
|
||||
Modify | 154.16 | 154.17 | 154.18 | 0.1 | 99.81
|
||||
Other | | 0.1998 | | | 0.13
|
||||
|
||||
Nlocal: 1 ave 4 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 3 ave 4 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 1.5 ave 6 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 6
|
||||
Ave neighs/atom = 1.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
#run 100000
|
||||
|
||||
Total wall time: 0:02:34
|
||||
@ -1,75 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.008 seconds
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
1 rigid bodies with 4 atoms
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.00025
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:739)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.763 | 6.857 | 7.138 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 2.1529156e-12
|
||||
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
|
||||
Loop time of 146.77 on 4 procs for 10000 steps with 4 atoms
|
||||
|
||||
Performance: 1471.691 ns/day, 0.016 hours/ns, 68.134 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.013542 | 0.017622 | 0.022577 | 2.8 | 0.01
|
||||
Bond | 0.001794 | 0.0018995 | 0.0021441 | 0.3 | 0.00
|
||||
Neigh | 6.97e-05 | 0.00011273 | 0.0001386 | 0.0 | 0.00
|
||||
Comm | 0.10125 | 0.13954 | 0.17353 | 7.3 | 0.10
|
||||
Output | 6.19e-05 | 0.00030725 | 0.0003896 | 0.0 | 0.00
|
||||
Modify | 146.37 | 146.4 | 146.45 | 0.2 | 99.75
|
||||
Other | | 0.2122 | | | 0.14
|
||||
|
||||
Nlocal: 1.00000 ave 4 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 3.00000 ave 4 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 1.50000 ave 6 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 6
|
||||
Ave neighs/atom = 1.5000000
|
||||
Ave special neighs/atom = 0.0000000
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 25.615363
|
||||
LB update time: 62.136116
|
||||
LB PCalc time: 36.863810
|
||||
LB fluidForce time: 11.645698
|
||||
LB CorrectU time: 9.399909
|
||||
Total wall time: 0:02:26
|
||||
Reference in New Issue
Block a user