Unverified Commit dbd458e9 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

update micelle example with corrected data file and rigid body input

parent 6e7f13e6

examples/micelle/data.micelle

+1537 −1528

File changed.

Preview size limit exceeded, changes collapsed.

examples/micelle/in.micelle-rigid

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Original line number Diff line number Diff line 
# 2d micelle simulation



dimension	2



neighbor	0.3 bin

neigh_modify	delay 5



atom_style	bond



# Soft potential push-off



read_data	data.micelle

special_bonds	fene



pair_style	soft 1.12246

pair_coeff	* * 0.0 1.12246



bond_style 	harmonic

bond_coeff	1 50.0 0.75



velocity	all create 0.45 2349852



variable	prefactor equal ramp(1.0,20.0)



fix		1 all nve

fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0

fix		3 all adapt 1 pair soft a * * v_prefactor

fix		4 all enforce2d



thermo		50

run		1000



unfix		3



# Main run



pair_style	lj/cut 2.5



# solvent/head - full-size and long-range



pair_coeff	1 1 1.0 1.0 2.5

pair_coeff	2 2 1.0 1.0 2.5

pair_coeff	1 2 1.0 1.0 2.5



# tail/tail - size-averaged and long-range



pair_coeff	3 3 1.0 0.75 2.5

pair_coeff	4 4 1.0 0.50 2.5

pair_coeff	3 4 1.0 0.67 2.5



# solvent/tail - full-size and repulsive



pair_coeff	1 3 1.0 1.0 1.12246

pair_coeff	1 4 1.0 1.0 1.12246



# head/tail - size-averaged and repulsive



pair_coeff	2 3 1.0 0.88 1.12246

pair_coeff	2 4 1.0 0.75 1.12246



thermo		1000



#dump		1 all atom 2000 dump.micelle



#dump		2 all image 2000 image.*.jpg type type zoom 1.6

#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75



#dump		3 all movie 2000 movie.mpg type type zoom 1.6

#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75



reset_timestep	0

group solvent   molecule 0

group solute    subtract all solvent

unfix 1

unfix 2

unfix 4

fix		1 solvent nve

fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0

fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211

fix		4 all enforce2d

run		20000

unfix 5

unfix 4

fix		5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211

fix		4 all enforce2d

run		20000

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

deleted100644 → 0
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Original line number Diff line number Diff line 
LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# 2d micelle simulation



dimension	2



neighbor	0.3 bin

neigh_modify	delay 5



atom_style	bond



# Soft potential push-off



read_data	data.micelle

  orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)

  2 by 2 by 1 MPI processor grid

  reading atoms ...

  1200 atoms

  scanning bonds ...

  1 = max bonds/atom

  reading bonds ...

  300 bonds

  2 = max # of 1-2 neighbors

  1 = max # of 1-3 neighbors

  1 = max # of 1-4 neighbors

  2 = max # of special neighbors

special_bonds	fene

  2 = max # of 1-2 neighbors

  2 = max # of special neighbors



pair_style	soft 1.12246

pair_coeff	* * 0.0 1.12246



bond_style 	harmonic

bond_coeff	1 50.0 0.75



velocity	all create 0.45 2349852



variable	prefactor equal ramp(1.0,20.0)



fix		1 all nve

fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0

fix		3 all adapt 1 pair soft a * * v_prefactor

fix		4 all enforce2d



thermo		50

run		1000

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 1.42246

  ghost atom cutoff = 1.42246

  binsize = 0.71123, bins = 51 51 1

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

  (1) pair soft, perpetual

      attributes: half, newton on

      pair build: half/bin/newton

      stencil: half/bin/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         0.45   0.40003481 2.2200223e-06   0.84966203   0.78952518 

      50   0.47411013   0.67721272  0.057404514    1.2083323    1.3375852 

     100         0.45   0.73046745  0.054836584     1.234929    2.3196516 

     150   0.67521742   0.72402001  0.043490075    1.4421648    2.8744416 

     200         0.45   0.78481891  0.076931503    1.3113754    3.0412388 

     250   0.66479018   0.69790602  0.081075564    1.4432178    3.6917024 

     300         0.45   0.76820218  0.066727591    1.2845548    3.7861054 

     350   0.67619136     0.625715  0.072722727    1.3740656    4.2861621 

     400         0.45   0.68527759  0.090724527    1.2256271    4.4725214 

     450   0.56702844   0.64402767  0.080555563    1.2911391    4.7402211 

     500         0.45   0.64883009  0.078376672    1.1768318    4.7919294 

     550     0.564664   0.58260368  0.080779475    1.2275766    4.9855705 

     600         0.45   0.58193041  0.088386617     1.119942     5.131481 

     650   0.52110993    0.5415273  0.097683746    1.1598867    5.2500294 

     700         0.45   0.50856787  0.088471208    1.0466641    5.2550165 

     750   0.51510855   0.47441291  0.089429375    1.0785216     5.375763 

     800         0.45   0.49926696  0.085958476    1.0348504    5.4665914 

     850   0.50688494   0.46614429  0.088962292    1.0615691     5.556932 

     900         0.45   0.47785593   0.10150857    1.0289895    5.7765975 

     950   0.49590559   0.46050477  0.096404887     1.052402    5.8649245 

    1000         0.45   0.47691182   0.08808163    1.0146185    6.0177568 

Loop time of 0.0641922 on 4 procs for 1000 steps with 1200 atoms



Performance: 6729792.131 tau/day, 15578.223 timesteps/s

90.9% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.020663   | 0.021445   | 0.022477   |   0.5 | 33.41

Bond    | 0.0014422  | 0.0015128  | 0.001569   |   0.1 |  2.36

Neigh   | 0.0067129  | 0.0067645  | 0.0068202  |   0.1 | 10.54

Comm    | 0.018454   | 0.019275   | 0.020386   |   0.5 | 30.03

Output  | 0.00038171 | 0.00040019 | 0.00044632 |   0.0 |  0.62

Modify  | 0.010561   | 0.010904   | 0.011309   |   0.3 | 16.99

Other   |            | 0.003891   |            |       |  6.06



Nlocal:    300 ave 305 max 292 min

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

Nghost:    100.25 ave 108 max 93 min

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

Neighs:    784 ave 815 max 739 min

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



Total # of neighbors = 3136

Ave neighs/atom = 2.61333

Ave special neighs/atom = 0.5

Neighbor list builds = 92

Dangerous builds = 0



unfix		3



# Main run



pair_style	lj/cut 2.5



# solvent/head - full-size and long-range



pair_coeff	1 1 1.0 1.0 2.5

pair_coeff	2 2 1.0 1.0 2.5

pair_coeff	1 2 1.0 1.0 2.5



# tail/tail - size-averaged and long-range



pair_coeff	3 3 1.0 0.75 2.5

pair_coeff	4 4 1.0 0.50 2.5

pair_coeff	3 4 1.0 0.67 2.5



# solvent/tail - full-size and repulsive



pair_coeff	1 3 1.0 1.0 1.12246

pair_coeff	1 4 1.0 1.0 1.12246



# head/tail - size-averaged and repulsive



pair_coeff	2 3 1.0 0.88 1.12246

pair_coeff	2 4 1.0 0.75 1.12246



thermo		1000



#dump		1 all atom 2000 dump.micelle



#dump		2 all image 2000 image.*.jpg type type zoom 1.6

#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75



#dump		3 all movie 2000 movie.mpg type type zoom 1.6

#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75



reset_timestep	0

run		60000

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4, bins = 26 26 1

  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/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         0.45   -1.7056163   0.08808163   -1.1679097    3.9431686 

    1000         0.45   -1.9727661   0.05860859   -1.4645325    1.9982402 

    2000   0.45146247   -1.9766043  0.059408886   -1.4661092    1.7398826 

    3000   0.43338517   -2.0028125  0.059884381   -1.5099041    1.4716488 

    4000   0.46674519   -2.0200954  0.066548679   -1.4871905    1.2506693 

    5000         0.45   -2.0207125  0.055926205   -1.5151613    1.3047457 

    6000   0.45447759   -2.0585234  0.068004883   -1.5364197    1.1859762 

    7000   0.43183018   -2.0170545  0.060800296   -1.5247839    1.3074223 

    8000   0.46657547    -2.053224  0.063224367    -1.523813    1.1785643 

    9000         0.45   -2.0691221  0.054959029    -1.564538    1.1833657 

   10000    0.4428252   -2.0473987  0.054306905   -1.5506356     1.181794 

   11000   0.45407036   -2.0746151  0.065849667   -1.5550734    1.1008545 

   12000   0.46061944   -2.0580809  0.063129643   -1.5347156    1.0206491 

   13000   0.45159068   -2.0640832  0.060059758   -1.5528091    1.0813494 

   14000   0.44141594   -2.0467255  0.062785088   -1.5428923    1.1465772 

   15000     0.454361   -2.0908595  0.057471037   -1.5794061   0.84297781 

   16000   0.44061091   -2.0521452  0.064644196   -1.5472573    1.1478647 

   17000   0.45118383    -2.081348  0.058660999   -1.5718791    1.0101404 

   18000   0.44664866   -2.0845745  0.060435731   -1.5778623   0.96142277 

   19000   0.45515339   -2.0914006  0.062174016   -1.5744525   0.87623323 

   20000   0.45624408   -2.0837697  0.059263054   -1.5686428   0.92810644 

   21000   0.46791657   -2.1062007  0.067355929   -1.5713181   0.88318793 

   22000   0.43907391   -2.1005271  0.065885144   -1.5959339   0.77211644 

   23000   0.43967354   -2.0723459  0.057613471   -1.5754253    1.0371548 

   24000   0.45716384   -2.0987126  0.055157377   -1.5867723   0.89670061 

   25000   0.45828285   -2.1041616  0.057736138   -1.5885245   0.79952286 

   26000         0.45   -2.0743463  0.072455519   -1.5522658   0.88260204 

   27000   0.46581599   -2.0804974  0.058113258   -1.5569564   0.93053891 

   28000   0.46904194   -2.0920124  0.059748792   -1.5636125   0.79359618 

   29000   0.46093196    -2.118556  0.063942334   -1.5940659   0.67707604 

   30000   0.45733724   -2.1197827  0.066939064   -1.5958875   0.66886075 

   31000   0.44580762   -2.0977175  0.056969121   -1.5953123   0.81042562 

   32000   0.44403029   -2.1032264  0.063465127    -1.596101   0.71796412 

   33000   0.45834072   -2.0934132  0.066035391    -1.569419   0.77873998 

   34000   0.44981563   -2.0910902   0.07138738   -1.5702621   0.75679805 

   35000   0.45383392   -2.0926654  0.067553478   -1.5716562    0.9064517 

   36000   0.44447198   -2.1107114  0.062718917   -1.6038909    0.8538349 

   37000   0.45838527   -2.1166464  0.062442606   -1.5962005    0.7300635 

   38000   0.45014075   -2.1096258  0.059293718   -1.6005665   0.73988246 

   39000   0.44377026    -2.080309  0.063545781   -1.5733628   0.99775641 

   40000   0.44577324   -2.1134607  0.065271179   -1.6027878   0.64113168 

   41000         0.45   -2.0937983  0.060881377   -1.5832919   0.78849829 

   42000   0.46866695   -2.1142283  0.056417605   -1.5895343   0.73788436 

   43000   0.43211727   -2.0819893  0.061463358   -1.5887688   0.95853724 

   44000   0.44138397   -2.0921314  0.059643895   -1.5914713   0.89486208 

   45000         0.45    -2.117209  0.054804331   -1.6127797   0.78564885 

   46000   0.44285245   -2.1090975  0.057629006   -1.6089851   0.64549424 

   47000   0.45537009   -2.1164296  0.068582324   -1.5928567   0.73629413 

   48000   0.45046732   -2.1006362  0.057249591   -1.5932947   0.74317593 

   49000   0.45425966   -2.1191703  0.064247719   -1.6010414   0.70962368 

   50000   0.45506149   -2.1184671  0.064911797   -1.5988731   0.69958156 

   51000   0.46047417   -2.1019719  0.058468259   -1.5834132   0.87219271 

   52000   0.43808317    -2.092294  0.057280941    -1.597295   0.84156893 

   53000   0.45012337   -2.1175234  0.064002667   -1.6037725   0.64562439 

   54000   0.43854679   -2.1236444  0.061316257   -1.6241468   0.72478117 

   55000   0.46382438   -2.1016563  0.060724666   -1.5774938   0.83311209 

   56000   0.44951533   -2.0946157  0.055075217   -1.5903998   0.90066109 

   57000   0.45937401   -2.0983442  0.061558996    -1.577794   0.58606161 

   58000     0.446669   -2.1146838  0.062385166   -1.6060019   0.73443388 

   59000   0.43847747   -2.1197461  0.060460257   -1.6211738    0.7230937 

   60000   0.45294215   -2.1258513  0.061895006   -1.6113915   0.70722168 

Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms



Performance: 5681397.232 tau/day, 13151.382 timesteps/s

97.1% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 2.2114     | 2.2527     | 2.3592     |   4.1 | 49.38

Bond    | 0.083713   | 0.09234    | 0.10244    |   2.3 |  2.02

Neigh   | 0.72491    | 0.7277     | 0.72957    |   0.2 | 15.95

Comm    | 0.79464    | 0.90036    | 0.94957    |   6.5 | 19.74

Output  | 0.0014119  | 0.0024976  | 0.0057502  |   3.8 |  0.05

Modify  | 0.33757    | 0.35202    | 0.36946    |   2.1 |  7.72

Other   |            | 0.2346     |            |       |  5.14



Nlocal:    300 ave 306 max 289 min

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

Nghost:    227.25 ave 250 max 216 min

Histogram: 2 0 1 0 0 0 0 0 0 1

Neighs:    2373.25 ave 2489 max 2283 min

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



Total # of neighbors = 9493

Ave neighs/atom = 7.91083

Ave special neighs/atom = 0.5

Neighbor list builds = 4888

Dangerous builds = 0

Total wall time: 0:00:04

examples/micelle/log.28Feb2019.micelle-rigid.g++.1

0 → 100644
+286 −0
Original line number Diff line number Diff line 
LAMMPS (28 Feb 2019)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)

  using 1 OpenMP thread(s) per MPI task

# 2d micelle simulation



dimension	2



neighbor	0.3 bin

neigh_modify	delay 5



atom_style	bond



# Soft potential push-off



read_data	data.micelle

  orthogonal box = (-0.39293 -0.050929 -0.1) to (35.4639 35.8059 0.1)

  1 by 1 by 1 MPI processor grid

  reading atoms ...

  1200 atoms

  scanning bonds ...

  1 = max bonds/atom

  reading bonds ...

  300 bonds

  2 = max # of 1-2 neighbors

  1 = max # of 1-3 neighbors

  1 = max # of 1-4 neighbors

  2 = max # of special neighbors

special_bonds	fene

  2 = max # of 1-2 neighbors

  2 = max # of special neighbors



pair_style	soft 1.12246

pair_coeff	* * 0.0 1.12246



bond_style 	harmonic

bond_coeff	1 50.0 0.75



velocity	all create 0.45 2349852



variable	prefactor equal ramp(1.0,20.0)



fix		1 all nve

fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0

fix		3 all adapt 1 pair soft a * * v_prefactor

fix		4 all enforce2d



thermo		50

run		1000

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 1.42246

  ghost atom cutoff = 1.42246

  binsize = 0.71123, bins = 51 51 1

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

  (1) pair soft, perpetual

      attributes: half, newton on

      pair build: half/bin/newton

      stencil: half/bin/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         0.45   0.40179153  0.017198847   0.86861538   0.75625658 

      50    0.4900086   0.67873245  0.060027837    1.2283605    1.3564879 

     100         0.45   0.73189198  0.056737309    1.2382543     2.321972 

     150   0.67879051   0.72086182  0.047167282     1.446254    2.8618146 

     200         0.45   0.78767975  0.079977445    1.3172822    3.0463605 

     250   0.66920583   0.70051688  0.080338407    1.4495034    3.6886758 

     300         0.45   0.76847924  0.069944127    1.2880484    3.7420091 

     350   0.68081034   0.62208465   0.07485122    1.3771789    4.2772161 

     400         0.45   0.69469019  0.094115526    1.2384307    4.4786122 

     450   0.58484619   0.64001545  0.080279506    1.3046538    4.7171436 

     500         0.45   0.64066675  0.080351857    1.1706436    4.7965076 

     550   0.56464426   0.57619219  0.080291646    1.2206576     4.926662 

     600         0.45   0.58371075  0.088545932    1.1218817    5.0963739 

     650   0.53299132   0.54564667  0.084628459    1.1628223    5.2932897 

     700         0.45    0.5394553   0.10365542    1.0927357    5.3370157 

     750   0.55102913   0.48080137  0.093062502    1.1244338    5.3005553 

     800         0.45   0.51563293    0.1030928    1.0683507    5.5156219 

     850   0.51623625    0.4768524   0.10367899    1.0963375    5.5799809 

     900         0.45    0.4758065  0.098479812    1.0239113    5.6783722 

     950   0.49518604   0.45196847   0.10031719     1.047059    5.8438261 

    1000         0.45   0.45306784  0.094144249   0.99683709    5.8485623 

Loop time of 0.108068 on 1 procs for 1000 steps with 1200 atoms



Performance: 3997492.279 tau/day, 9253.454 timesteps/s

99.9% CPU use with 1 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.071711   | 0.071711   | 0.071711   |   0.0 | 66.36

Bond    | 0.0039465  | 0.0039465  | 0.0039465  |   0.0 |  3.65

Neigh   | 0.01743    | 0.01743    | 0.01743    |   0.0 | 16.13

Comm    | 0.0018625  | 0.0018625  | 0.0018625  |   0.0 |  1.72

Output  | 0.00015855 | 0.00015855 | 0.00015855 |   0.0 |  0.15

Modify  | 0.01058    | 0.01058    | 0.01058    |   0.0 |  9.79

Other   |            | 0.00238    |            |       |  2.20



Nlocal:    1200 ave 1200 max 1200 min

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

Nghost:    206 ave 206 max 206 min

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

Neighs:    3191 ave 3191 max 3191 min

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



Total # of neighbors = 3191

Ave neighs/atom = 2.65917

Ave special neighs/atom = 0.5

Neighbor list builds = 99

Dangerous builds = 0



unfix		3



# Main run



pair_style	lj/cut 2.5



# solvent/head - full-size and long-range



pair_coeff	1 1 1.0 1.0 2.5

pair_coeff	2 2 1.0 1.0 2.5

pair_coeff	1 2 1.0 1.0 2.5



# tail/tail - size-averaged and long-range



pair_coeff	3 3 1.0 0.75 2.5

pair_coeff	4 4 1.0 0.50 2.5

pair_coeff	3 4 1.0 0.67 2.5



# solvent/tail - full-size and repulsive



pair_coeff	1 3 1.0 1.0 1.12246

pair_coeff	1 4 1.0 1.0 1.12246



# head/tail - size-averaged and repulsive



pair_coeff	2 3 1.0 0.88 1.12246

pair_coeff	2 4 1.0 0.75 1.12246



thermo		1000



#dump		1 all atom 2000 dump.micelle



#dump		2 all image 2000 image.*.jpg type type zoom 1.6

#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75



#dump		3 all movie 2000 movie.mpg type type zoom 1.6

#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75



reset_timestep	0

group solvent   molecule 0

0 atoms in group solvent

group solute    subtract all solvent

1200 atoms in group solute

unfix 1

unfix 2

unfix 4

fix		1 solvent nve

fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0

fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211

151 rigid bodies with 1200 atoms

fix		4 all enforce2d

run		20000

Neighbor list info ...

  update every 1 steps, delay 5 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4, bins = 26 26 1

  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/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0   0.43824398   -1.7061976  0.094144249      -1.5297    35.328657 

    1000   0.44980495   -1.7618752  0.094144249   -1.5832051  -0.78239121 

    2000    0.4080548   -1.7592744  0.094144249   -1.5884498    3.7941359 

    3000   0.43543409   -1.7704837  0.094144249   -1.5945142    2.0801732 

    4000   0.43624218   -1.7752975  0.094144249   -1.5991761    5.3401997 

    5000   0.44526204   -1.7627039  0.094144249   -1.5848875    1.8074242 

    6000   0.45601171   -1.7578409  0.094144249   -1.5780044    3.6999235 

    7000   0.45000311   -1.7707158  0.094144249   -1.5920085    14.198063 

    8000   0.49199853   -1.7647643  0.094144249   -1.5781653    1.1767602 

    9000   0.42662498   -1.7719397  0.094144249   -1.5976255    1.8316615 

   10000   0.44225069   -1.7704012  0.094144249   -1.5931507    4.2515329 

   11000   0.54415369   -1.7634927  0.094144249   -1.5670929     7.626065 

   12000   0.42501235   -1.7698463  0.094144249   -1.5958351    1.4118043 

   13000   0.48382538   -1.7497323  0.094144249   -1.5646692    2.2441707 

   14000    0.4376704   -1.7658795  0.094144249   -1.5894897    2.7170856 

   15000   0.42644426    -1.758103  0.094144249   -1.5838228    5.6129465 

   16000   0.37371943   -1.7881668  0.094144249   -1.6237944    4.0731922 

   17000   0.42320956   -1.7831129  0.094144249   -1.6094406   -4.2042077 

   18000   0.47319029   -1.7642512  0.094144249   -1.5811866    1.8859862 

   19000   0.45117547   -1.7736983  0.094144249   -1.5947706   -1.3566752 

   20000   0.48993295   -1.7820573  0.094144249   -1.5958465  -0.63347623 

Loop time of 3.56168 on 1 procs for 20000 steps with 1200 atoms



Performance: 2425823.418 tau/day, 5615.332 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    | 1.7048     | 1.7048     | 1.7048     |   0.0 | 47.86

Bond    | 0.079658   | 0.079658   | 0.079658   |   0.0 |  2.24

Neigh   | 0.36319    | 0.36319    | 0.36319    |   0.0 | 10.20

Comm    | 0.042085   | 0.042085   | 0.042085   |   0.0 |  1.18

Output  | 0.00021696 | 0.00021696 | 0.00021696 |   0.0 |  0.01

Modify  | 1.3169     | 1.3169     | 1.3169     |   0.0 | 36.97

Other   |            | 0.05485    |            |       |  1.54



Nlocal:    1200 ave 1200 max 1200 min

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

Nghost:    414 ave 414 max 414 min

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

Neighs:    8824 ave 8824 max 8824 min

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



Total # of neighbors = 8824

Ave neighs/atom = 7.35333

Ave special neighs/atom = 0.5

Neighbor list builds = 1148

Dangerous builds = 0

unfix 5

unfix 4

fix		5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211

151 rigid bodies with 1200 atoms

  25.2208 = max distance from body owner to body atom

fix		4 all enforce2d

run		20000

Per MPI rank memory allocation (min/avg/max) = 8.642 | 8.642 | 8.642 Mbytes

Step Temp E_pair E_mol TotEng Press 

   20000   0.48993295   -1.7820573  0.094144249   -1.5958465     3.267595 

   21000   0.42136691   -1.7767171  0.094144249   -1.6033909    1.1186996 

   22000   0.42456205   -1.7606471  0.094144249   -1.5867205    2.8866506 

   23000   0.48026533   -1.7693864  0.094144249   -1.5849923    7.3708907 

   24000   0.51908347   -1.7748052  0.094144249   -1.5831165  -0.88177558 

   25000   0.46033763   -1.7615973  0.094144249    -1.580948    7.0803034 

   26000   0.48667124   -1.7625783  0.094144249   -1.5769804   -11.557404 

   27000   0.45085745   -1.7833193  0.094144249   -1.6044514    6.5390499 

   28000   0.47333185   -1.7561049  0.094144249   -1.5730137   -3.2587604 

   29000   0.46380712   -1.7830962  0.094144249   -1.6017949    7.1120026 

   30000   0.41845082   -1.7808054  0.094144249   -1.6080272    3.6435588 

   31000     0.510966   -1.7649896  0.094144249   -1.5748263    1.4979844 

   32000   0.42169482   -1.7623593  0.094144249   -1.5889716    2.6130718 

   33000   0.43724881    -1.769415  0.094144249   -1.5931044    1.1205627 

   34000   0.43753147   -1.7878022  0.094144249   -1.6114385    9.0463054 

   35000   0.44230686   -1.7554417  0.094144249   -1.5781806     3.776513 

   36000   0.39564972   -1.7614398  0.094144249   -1.5929464    4.6243057 

   37000   0.39176208   -1.7586072  0.094144249   -1.5908443   -2.1444581 

   38000    0.4601972   -1.7727349  0.094144249   -1.5921119     9.513042 

   39000   0.42107042   -1.7703643  0.094144249   -1.5970939    5.3409161 

   40000   0.45100889   -1.7794839  0.094144249   -1.6005876   -8.2877164 

Loop time of 3.5613 on 1 procs for 20000 steps with 1200 atoms



Performance: 2426077.738 tau/day, 5615.921 timesteps/s

99.9% CPU use with 1 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 1.7113     | 1.7113     | 1.7113     |   0.0 | 48.05

Bond    | 0.079594   | 0.079594   | 0.079594   |   0.0 |  2.23

Neigh   | 0.36249    | 0.36249    | 0.36249    |   0.0 | 10.18

Comm    | 0.042057   | 0.042057   | 0.042057   |   0.0 |  1.18

Output  | 0.00020933 | 0.00020933 | 0.00020933 |   0.0 |  0.01

Modify  | 1.3102     | 1.3102     | 1.3102     |   0.0 | 36.79

Other   |            | 0.05553    |            |       |  1.56



Nlocal:    1200 ave 1200 max 1200 min

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

Nghost:    405 ave 405 max 405 min

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

Neighs:    8806 ave 8806 max 8806 min

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



Total # of neighbors = 8806

Ave neighs/atom = 7.33833

Ave special neighs/atom = 0.5

Neighbor list builds = 1149

Dangerous builds = 0

Total wall time: 0:00:07

examples/micelle/log.28Feb2019.micelle-rigid.g++.4

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+286 −0

File added.

Preview size limit exceeded, changes collapsed.

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