Commit 85291698 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

update logs for colloid example

parent d0a83e9e

examples/colloid/log.27Nov18.colloid.g++.1

0 → 100644
+153 −0
Original line number Diff line number Diff line 
LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# Big colloid particles and small LJ particles



units		lj

atom_style	sphere

dimension	2



lattice		sq 0.01

Lattice spacing in x,y,z = 10 10 10

region		box block 0 30 0 30 -0.5 0.5

create_box	2 box

Created orthogonal box = (0 0 -5) to (300 300 5)

  1 by 1 by 1 MPI processor grid

create_atoms	1 box

Created 900 atoms

  Time spent = 0.000598431 secs



set		group all type/fraction 2 0.96 23984

  861 settings made for type/fraction



set		type 1 mass 9

  39 settings made for mass

set		type 2 mass 1

  861 settings made for mass



velocity	all create 1.44 87287 loop geom



# multi neighbor and comm for efficiency



neighbor	1 multi

neigh_modify	delay 0

comm_modify     mode multi



# colloid potential



pair_style	colloid 12.5

pair_coeff	1 1  1.0 1.0 5.0 5.0 12.5

pair_coeff	1 2  5.0 1.0 5.0 0.0 7.0

pair_coeff	2 2 10.0 1.0 0.0 0.0 2.5



fix		1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 	        mtk no pchain 0 tchain 1

fix		2 all enforce2d



#dump		1 all atom 1000 dump.colloid



#dump		2 all image 1000 image.*.jpg type type #		zoom 1.5 center d 0.5 0.5 0.5

#dump_modify	2 pad 5 adiam 1 5.0 adiam 2 1.5



#dump		3 all movie 1000 movie.mpg type type #		zoom 1.5 center d 0.5 0.5 0.5

#dump_modify	3 pad 5 adiam 1 5.0 adiam 2 1.5



thermo_style	custom step temp epair etotal press vol

thermo		1000



timestep	0.005



run		50000

Neighbor list info ...

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 13.5

  ghost atom cutoff = 13.5

  binsize = 1.75, bins = 172 172 6

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair colloid, perpetual

      attributes: half, newton on

      pair build: half/multi/newton

      stencil: half/multi/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 4.445 | 4.445 | 4.445 Mbytes

Step Temp E_pair TotEng Press Volume 

       0         1.44 -2.2136534e-06    1.4383978  0.014383923        90000 

    1000    1.9572809 -0.00036743274    1.9547388  0.017982269    98935.161 

    2000     2.068567 -0.0010518227    2.0652168  0.019466739    96307.439 

    3000    2.1787472 0.0045846363     2.180911  0.029249545     68560.31 

    4000    2.1979309 0.0017234058    2.1972121  0.048831814    42699.657 

    5000    2.1541368 0.0068842503    2.1586276   0.07471981    28571.492 

    6000    2.1113173 0.0024196693    2.1113911  0.091799816     21611.61 

    7000    2.0788416 0.0060975475    2.0826293   0.11638141    17868.699 

    8000    2.0587325  0.011431711    2.0678767     0.136977    15515.134 

    9000    2.0608274 0.00084150047    2.0593791    0.1448357    13890.944 

   10000    2.0446145  0.016230031    2.0585728   0.17785946    12557.927 

   11000    2.0481772  0.008961682    2.0548631    0.1925805    11482.879 

   12000    2.0536702 0.0065675004    2.0579558   0.19987216    10543.356 

   13000    2.0483659 0.0071445135    2.0532344   0.22867229     9777.939 

   14000    2.0334727  0.020440289    2.0516536   0.25700656    9138.0619 

   15000    2.0221794  0.032212195    2.0521448   0.28477019    8585.7952 

   16000     2.029058  0.024040298    2.0508438   0.28585812    8095.1269 

   17000    2.0270567  0.025118634     2.049923   0.30905216    7689.7819 

   18000    2.0123899  0.037421737    2.0475757    0.3636938    7364.3469 

   19000     2.019082  0.032220518    2.0490591   0.35887838    7063.0831 

   20000    2.0383387  0.013928928    2.0500028   0.35029696    6810.6189 

   21000    2.0113975  0.039874446    2.0490371   0.41652382     6555.842 

   22000    2.0292399  0.029463117    2.0564483   0.40823941    6292.2335 

   23000    2.0271279  0.033537888    2.0584134    0.4359853    6051.2547 

   24000    2.0075928  0.044388917    2.0497511   0.46590892      5890.69 

   25000    2.0345451  0.017490239    2.0497748   0.44508598    5798.4911 

   26000    1.9933171  0.070984054    2.0620863   0.53325353     5618.279 

   27000    2.0437208  0.022615819    2.0640658   0.50130607    5440.3246 

   28000    2.0101461  0.054907742    2.0628204   0.55318766    5304.6714 

   29000    2.0231122  0.043194685    2.0640589   0.54438745    5197.9144 

   30000    2.0036611  0.062982451    2.0644173    0.5791539    5071.4318 

   31000    2.0118619  0.055674047    2.0653006   0.63370324    4956.3038 

   32000    2.0291738  0.035314054    2.0622333   0.59475403    4852.8359 

   33000    1.9954345  0.075707165    2.0689245    0.6809065    4761.5146 

   34000    2.0141897   0.04990827    2.0618599   0.61183102    4681.1535 

   35000    2.0002914  0.072549616    2.0706185   0.78205667    4595.2138 

   36000    2.0048956  0.065248982     2.067917   0.74763198    4502.7759 

   37000    2.0229016  0.049698006     2.070352    0.6949933    4422.5382 

   38000    2.0291924  0.048408539    2.0753463   0.67746901    4353.6336 

   39000    2.0057251  0.071071345    2.0745679     0.781985    4293.9239 

   40000    2.0314588  0.052600075    2.0818017   0.71759858    4247.5894 

   41000    2.0229153  0.059717009    2.0803846   0.73068778    4179.9404 

   42000     2.003508  0.080215578    2.0814975   0.81505369    4124.3279 

   43000    2.0034351  0.079898162    2.0811072   0.81862672    4075.4928 

   44000    2.0151423  0.074554369    2.0874576   0.84679645    4014.0973 

   45000    2.0210784  0.073589668    2.0924224   0.82507573    3960.3663 

   46000    2.0192162  0.069599489    2.0865721   0.87813695     3915.513 

   47000     2.019728  0.071103706    2.0885875   0.90918917    3864.3408 

   48000    2.0138563  0.073940136    2.0855588   0.86312211    3819.3487 

   49000    2.0257679  0.066368453    2.0898855   0.99155677    3794.5614 

   50000    2.0054884  0.089153801    2.0924139   0.99114819    3770.4528 

Loop time of 9.13278 on 1 procs for 50000 steps with 900 atoms



Performance: 2365106.031 tau/day, 5474.782 timesteps/s

99.8% CPU use with 1 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 4.0125     | 4.0125     | 4.0125     |   0.0 | 43.93

Neigh   | 1.4242     | 1.4242     | 1.4242     |   0.0 | 15.59

Comm    | 0.45633    | 0.45633    | 0.45633    |   0.0 |  5.00

Output  | 0.00083971 | 0.00083971 | 0.00083971 |   0.0 |  0.01

Modify  | 2.8978     | 2.8978     | 2.8978     |   0.0 | 31.73

Other   |            | 0.3412     |            |       |  3.74



Nlocal:    900 ave 900 max 900 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    571 ave 571 max 571 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    5952 ave 5952 max 5952 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 5952

Ave neighs/atom = 6.61333

Neighbor list builds = 3099

Dangerous builds = 0



Please see the log.cite file for references relevant to this simulation



Total wall time: 0:00:09

examples/colloid/log.27Nov18.colloid.g++.4

0 → 100644
+153 −0
Original line number Diff line number Diff line 
LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# Big colloid particles and small LJ particles



units		lj

atom_style	sphere

dimension	2



lattice		sq 0.01

Lattice spacing in x,y,z = 10 10 10

region		box block 0 30 0 30 -0.5 0.5

create_box	2 box

Created orthogonal box = (0 0 -5) to (300 300 5)

  2 by 2 by 1 MPI processor grid

create_atoms	1 box

Created 900 atoms

  Time spent = 0.000492334 secs



set		group all type/fraction 2 0.96 23984

  861 settings made for type/fraction



set		type 1 mass 9

  39 settings made for mass

set		type 2 mass 1

  861 settings made for mass



velocity	all create 1.44 87287 loop geom



# multi neighbor and comm for efficiency



neighbor	1 multi

neigh_modify	delay 0

comm_modify     mode multi



# colloid potential



pair_style	colloid 12.5

pair_coeff	1 1  1.0 1.0 5.0 5.0 12.5

pair_coeff	1 2  5.0 1.0 5.0 0.0 7.0

pair_coeff	2 2 10.0 1.0 0.0 0.0 2.5



fix		1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 	        mtk no pchain 0 tchain 1

fix		2 all enforce2d



#dump		1 all atom 1000 dump.colloid



#dump		2 all image 1000 image.*.jpg type type #		zoom 1.5 center d 0.5 0.5 0.5

#dump_modify	2 pad 5 adiam 1 5.0 adiam 2 1.5



#dump		3 all movie 1000 movie.mpg type type #		zoom 1.5 center d 0.5 0.5 0.5

#dump_modify	3 pad 5 adiam 1 5.0 adiam 2 1.5



thermo_style	custom step temp epair etotal press vol

thermo		1000



timestep	0.005



run		50000

Neighbor list info ...

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 13.5

  ghost atom cutoff = 13.5

  binsize = 1.75, bins = 172 172 6

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair colloid, perpetual

      attributes: half, newton on

      pair build: half/multi/newton

      stencil: half/multi/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 4.344 | 4.344 | 4.345 Mbytes

Step Temp E_pair TotEng Press Volume 

       0         1.44 -2.2136534e-06    1.4383978  0.014383923        90000 

    1000    1.9572809 -0.00036743274    1.9547388  0.017982269    98935.161 

    2000     2.068567 -0.0010518227    2.0652168  0.019466739    96307.439 

    3000    2.1787472 0.0045846363     2.180911  0.029249545     68560.31 

    4000    2.1979309 0.0017234058    2.1972121  0.048831814    42699.657 

    5000    2.1541368 0.0068842504    2.1586276   0.07471981    28571.492 

    6000    2.1113175 0.0024194723    2.1113911  0.091799767     21611.61 

    7000    2.0788795 0.0060577432    2.0826274   0.11639395    17868.707 

    8000    2.0537762   0.01651572    2.0680099   0.13601134     15517.28 

    9000    2.0427394  0.019556597    2.0600262   0.15430942     13881.26 

   10000     2.050769  0.010396598     2.058887   0.16312819    12594.101 

   11000    2.0439348  0.018189464    2.0598533    0.2172647     11494.35 

   12000    2.0493504  0.010908719    2.0579821   0.21333624     10567.11 

   13000    2.0474606  0.013141328    2.0583269    0.2321885    9768.8239 

   14000    2.0370325  0.020936303    2.0557055   0.27034432    9105.9607 

   15000    2.0077835  0.045753549    2.0513062    0.3078643    8580.9799 

   16000    2.0184593  0.035585101    2.0518017   0.28738263    8120.9005 

   17000    2.0071721  0.044732393    2.0496743   0.32368949    7762.8875 

   18000    2.0085194  0.043117932    2.0494056   0.35526658    7442.6597 

   19000    2.0263547  0.029022667    2.0531258    0.3691966    7124.1683 

   20000    2.0285624   0.03264145    2.0589499   0.39783282    6810.1273 

   21000    2.0212924  0.039016129    2.0580626   0.42089074    6535.8717 

   22000    2.0285415  0.030259995    2.0565475   0.42080619    6301.8013 

   23000    2.0344885   0.02346797    2.0556959    0.4345206    6100.1797 

   24000    2.0219939  0.031317084    2.0510643   0.41301645    5921.1948 

   25000     2.034277  0.023680834    2.0556976   0.47443175    5749.5789 

   26000    2.0143035  0.051903569     2.063969   0.47278476    5570.3177 

   27000    2.0091763  0.054826231    2.0617701   0.53731629    5405.5081 

   28000    2.0306603  0.030512009     2.058916   0.50158605    5292.5739 

   29000    1.9905878  0.063609393    2.0519854   0.62105081    5217.6324 

   30000    2.0047307  0.057002418    2.0595056   0.59872107    5125.6009 

   31000    2.0076871  0.064365243    2.0698216   0.56914126    4971.7382 

   32000    2.0399769  0.031886115    2.0695964   0.55523269    4850.6347 

   33000    2.0196607  0.042847913    2.0602646    0.5749789    4770.7458 

   34000    2.0079696  0.067168038    2.0729066   0.70228842    4704.8088 

   35000    2.0264945  0.043126775    2.0673696   0.62754917    4625.3307 

   36000     2.029471  0.050993168    2.0782092   0.65985012    4513.2576 

   37000    2.0211356  0.053873626    2.0727635   0.75743646    4426.8691 

   38000    1.9933609   0.08028105    2.0714271     0.729473    4388.5022 

   39000    2.0046836  0.076855879     2.079312   0.83705993    4291.7229 

   40000    2.0321953  0.046360451    2.0762978   0.71726696    4229.9223 

   41000    2.0332458  0.051512927    2.0824996   0.78613181    4157.4167 

   42000    1.9750553  0.097198273    2.0700591   0.84569229    4123.0833 

   43000    2.0234742  0.056757566    2.0779835   0.78732804    4096.6281 

   44000    1.9966481  0.094296711    2.0887263   0.86811037    4021.0355 

   45000    2.0099144  0.077843813     2.085525   0.87222128    3961.2649 

   46000    1.9959281  0.090282388    2.0839928   0.90564582    3916.4041 

   47000    2.0174181  0.067872225    2.0830488   0.86559533    3889.8008 

   48000    2.0066047  0.094875259    2.0992504   0.99089696    3835.3328 

   49000    2.0031392  0.094024663    2.0949381    1.0600075    3789.3375 

   50000    2.0307693  0.059124989    2.0876379   0.85398261    3770.4556 

Loop time of 4.0156 on 4 procs for 50000 steps with 900 atoms



Performance: 5379021.062 tau/day, 12451.438 timesteps/s

94.8% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.8857     | 0.95678    | 0.99748    |   4.6 | 23.83

Neigh   | 0.34187    | 0.39239    | 0.42858    |   5.1 |  9.77

Comm    | 0.95431    | 1.0287     | 1.1204     |   6.3 | 25.62

Output  | 0.0010757  | 0.0037161  | 0.011632   |   7.5 |  0.09

Modify  | 1.3279     | 1.3522     | 1.3823     |   1.7 | 33.67

Other   |            | 0.2818     |            |       |  7.02



Nlocal:    225 ave 251 max 186 min

Histogram: 1 0 0 0 0 0 1 1 0 1

Nghost:    302.75 ave 330 max 288 min

Histogram: 1 1 1 0 0 0 0 0 0 1

Neighs:    1487.5 ave 1689 max 1191 min

Histogram: 1 0 0 0 0 1 0 0 1 1



Total # of neighbors = 5950

Ave neighs/atom = 6.61111

Neighbor list builds = 3097

Dangerous builds = 0



Please see the log.cite file for references relevant to this simulation



Total wall time: 0:00:04

examples/colloid/log.5Oct16.colloid.g++.1

deleted100644 → 0
+0 −146
Original line number Diff line number Diff line 
LAMMPS (5 Oct 2016)

# Big colloid particles and small LJ particles



units		lj

atom_style	sphere

dimension	2



lattice		sq 0.01

Lattice spacing in x,y,z = 10 10 10

region		box block 0 30 0 30 -0.5 0.5

create_box	2 box

Created orthogonal box = (0 0 -5) to (300 300 5)

  1 by 1 by 1 MPI processor grid

create_atoms	1 box

Created 900 atoms



set		group all type/fraction 2 0.96 23984

  861 settings made for type/fraction



set		type 1 mass 9

  39 settings made for mass

set		type 2 mass 1

  861 settings made for mass



velocity	all create 1.44 87287 loop geom



# multi neighbor and comm for efficiency



neighbor	1 multi

neigh_modify	delay 0

comm_modify     mode multi



# colloid potential



pair_style	colloid 12.5

pair_coeff	1 1  1.0 1.0 5.0 5.0 12.5

pair_coeff	1 2  5.0 1.0 5.0 0.0 7.0

pair_coeff	2 2 10.0 1.0 0.0 0.0 2.5



fix		1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 	        mtk no pchain 0 tchain 1

fix		2 all enforce2d



#dump		1 all atom 1000 dump.colloid



#dump		2 all image 1000 image.*.jpg type type #		zoom 1.5 center d 0.5 0.5 0.5

#dump_modify	2 pad 5 adiam 1 5.0 adiam 2 1.5



#dump		3 all movie 1000 movie.mpg type type #		zoom 1.5 center d 0.5 0.5 0.5

#dump_modify	3 pad 5 adiam 1 5.0 adiam 2 1.5



thermo_style	custom step temp epair etotal press vol

thermo		1000



timestep	0.005



run		50000

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 13.5

  ghost atom cutoff = 13.5

  binsize = 1.75 -> bins = 172 172 6

Memory usage per processor = 3.86192 Mbytes

Step Temp E_pair TotEng Press Volume 

       0         1.44 -2.2136534e-06    1.4383978  0.014383923        90000 

    1000    1.9572355 -0.00037176804     1.954689  0.017979461    98945.011 

    2000    2.0686234 -0.0010137498    2.0653112   0.01947028    96310.014 

    3000    2.1785689 0.0049562211    2.1811045  0.029298361     68537.78 

    4000     2.200053 0.00039100896    2.1979995  0.048071724    42672.579 

    5000    2.1407629  0.016107912    2.1544922  0.076141728      28576.1 

    6000    2.1131357 0.00050904012    2.1112969  0.095060602    21598.175 

    7000    2.0717026  0.013639823    2.0830406   0.11782618    17864.757 

    8000    2.0557671  0.015637275    2.0691201   0.13461012    15542.602 

    9000     2.052181  0.011294709    2.0611955   0.15150744    13852.149 

   10000    2.0531753  0.005995461    2.0568894   0.17005868    12487.961 

   11000    2.0458212  0.013960278    2.0575083   0.18853479     11391.15 

   12000    2.0405323   0.01846093     2.056726   0.20856764    10532.913 

   13000    2.0169788  0.041436672    2.0561744   0.23593917    9743.2413 

   14000    2.0381291  0.017030208    2.0528947   0.23907374     9093.804 

   15000    2.0400498  0.010140701    2.0479238   0.27667462    8571.3248 

   16000    2.0280005  0.024278921    2.0500261   0.31642444    8133.8701 

   17000    2.0330813  0.018237365    2.0490597   0.30128788    7764.8228 

   18000    2.0239878   0.02723825    2.0489771   0.30818234     7455.765 

   19000    2.0213402  0.035515393    2.0546096   0.39654991    7096.9286 

   20000     2.024466  0.032163441    2.0543801   0.37550172    6782.3498 

   21000     2.033932  0.017240839    2.0489129   0.39674508    6520.0345 

   22000    2.0204921  0.033630164    2.0518773   0.41617948    6306.7194 

   23000    2.0103922  0.046109389    2.0542679   0.44503939    6108.8439 

   24000    2.0063543  0.049507774    2.0536328    0.4949354    5923.2093 

   25000    1.9953872  0.066107231    2.0592773    0.5424389    5746.6695 

   26000    2.0416248  0.020853398    2.0602097   0.46642685    5593.8186 

   27000    2.0280574  0.037040684    2.0628447   0.49730884     5433.376 

   28000    2.0039648  0.055918617    2.0576568   0.56893257    5281.5584 

   29000    2.0042398  0.056161548    2.0581744   0.55361133    5164.0991 

   30000     2.031788  0.030776854    2.0603073   0.58478846    5056.2821 

   31000    2.0220647  0.044025601    2.0638435   0.60571441    4939.9798 

   32000    2.0115578    0.0548283     2.064151   0.62749615    4859.2601 

   33000    1.9905768  0.071616735    2.0599817   0.64066244    4787.7818 

   34000    2.0209823  0.052197269    2.0709341   0.68260584    4705.5825 

   35000     1.995165  0.078611977    2.0715601   0.69333031    4599.9346 

   36000     1.994471  0.079545726    2.0718006    0.7510532    4523.7494 

   37000    1.9939754  0.083417982    2.0751779   0.73746747    4449.8485 

   38000    1.9808613  0.098188975    2.0768493   0.89305039    4362.0588 

   39000    2.0056223  0.070537588    2.0739314   0.75049166     4320.201 

   40000    2.0490165  0.033488307    2.0802281   0.71809099    4259.8017 

   41000    2.0170375  0.066555481    2.0813519   0.80145545     4165.276 

   42000     2.034609  0.050123688     2.082472    0.7318767    4099.5342 

   43000     2.027217  0.053657298    2.0786218   0.79779536    4050.1962 

   44000    2.0107551   0.07427185    2.0827928   0.88949517    4022.2995 

   45000     2.035579  0.054511708     2.087829   0.85058092    3982.0592 

   46000    1.9855666    0.1079948    2.0913552   0.96268676     3937.279 

   47000    1.9938397  0.095380271    2.0870046   0.94036115    3882.9266 

   48000    2.0056151  0.087885527    2.0912722   0.94935203    3824.2309 

   49000    2.0079615  0.089440768    2.0951712   0.97596247    3781.8079 

   50000    1.9875181   0.10628651    2.0915963    1.1315334    3749.1501 

Loop time of 8.34943 on 1 procs for 50000 steps with 900 atoms



Performance: 2587004.175 tau/day, 5988.436 timesteps/s

99.9% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 3.9819     | 3.9819     | 3.9819     |   0.0 | 47.69

Neigh   | 1.3743     | 1.3743     | 1.3743     |   0.0 | 16.46

Comm    | 0.31324    | 0.31324    | 0.31324    |   0.0 |  3.75

Output  | 0.00052619 | 0.00052619 | 0.00052619 |   0.0 |  0.01

Modify  | 2.3748     | 2.3748     | 2.3748     |   0.0 | 28.44

Other   |            | 0.3047     |            |       |  3.65



Nlocal:    900 ave 900 max 900 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    548 ave 548 max 548 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    6073 ave 6073 max 6073 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 6073

Ave neighs/atom = 6.74778

Neighbor list builds = 3122

Dangerous builds = 0



Please see the log.cite file for references relevant to this simulation



Total wall time: 0:00:08

examples/colloid/log.5Oct16.colloid.g++.4

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