Commit 0d3cb6da authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4713 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 03568917

examples/colloid/log.colloid.10Sep10.linux.1

0 → 100644
+120 −0
Original line number Diff line number Diff line 
LAMMPS (10 Sep 2010)

# Big colloid particles and small LJ particles



units		lj

atom_style	atomic

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 processor grid

create_atoms	1 box

Created 900 atoms



set		group all type/fraction 2 0.96 23984

  861 settings made for type/fraction



mass		1 9

mass		2 1



velocity	all create 1.44 87287 loop geom



# multi neighbor and comm for efficiency



neighbor	1 multi

neigh_modify	delay 0

communicate	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 200 dump.colloid



thermo_style	custom step temp epair etotal press vol

thermo		1000



timestep	0.005



run		50000

Memory usage per processor = 1.84805 Mbytes

Step Temp E_pair TotEng Press Volume 

       0         1.44 -2.2136534e-06    1.4383978  0.014383923        90000 

    1000    1.9558819 -0.00044998322    1.9532587   0.01784589     99146.35 

    2000    2.0558568  0.011295331    2.0648679  0.021858185    96654.425 

    3000    2.1809647 0.0091754217    2.1877168  0.031294876     68756.47 

    4000    2.1960934 0.0028186107    2.1964719  0.049318667    42974.984 

    5000    2.1463273  0.012748525     2.156691  0.073994939    28660.577 

    6000    2.1073993 0.0076701766    2.1127279   0.09765596    21544.211 

    7000    2.0845784 -0.002231208     2.080031   0.11014385    17791.281 

    8000    2.0649566 0.0033946644    2.0660569   0.12813955    15494.971 

    9000    2.0549341 0.0036407503    2.0562916   0.14677203    13871.133 

   10000    2.0533504 0.0061906109    2.0572595   0.16609325    12575.783 

   11000    2.0512293 0.0054299129      2.05438   0.18469361    11512.707 

   12000    2.0417414  0.012714586    2.0521874   0.20813515    10612.626 

   13000    2.0340554  0.024863066    2.0566584   0.23789399    9831.2233 

   14000    2.0227138  0.031383229    2.0518496   0.26672609    9192.1178 

   15000    2.0461217   0.01108123    2.0549295   0.26343875    8634.5676 

   16000    2.0458851 0.0096312089    2.0532431   0.28019349    8142.3052 

   17000    2.0277001  0.025551945     2.050999   0.31081974    7748.6641 

   18000    2.0214721  0.032250275    2.0514763   0.33102736    7396.8201 

   19000    2.0363924  0.016941587    2.0510713   0.33406483    7060.7629 

   20000    2.0310397  0.023344929    2.0521279   0.35924735    6790.0327 

   21000     2.022195  0.033750346    2.0536984   0.39278369    6553.9448 

   22000    2.0125755  0.044598473    2.0549377   0.46764457    6324.4162 

   23000    2.0062096  0.049106575    2.0530871   0.45440086    6120.7099 

   24000    2.0179886  0.039373042    2.0551194   0.49940564    5909.9566 

   25000    2.0332507  0.025245421    2.0562369   0.45330345    5738.0889 

   26000    1.9964095  0.063580029    2.0577713   0.54097144    5578.2387 

   27000    2.0244455  0.038598397    2.0607945   0.52231996    5434.0327 

   28000    1.9938911  0.067766733    2.0594424   0.61091823    5292.7262 

   29000    2.0218405  0.036999202    2.0565932    0.5311977    5203.3778 

   30000    2.0207832  0.046760682    2.0652986   0.56610538    5070.3386 

   31000    1.9912351  0.078697601    2.0677202    0.6322967    4965.1486 

   32000    2.0238381  0.047492236    2.0690816   0.63381363    4835.9878 

   33000     2.039799  0.026525862    2.0640584   0.53285022    4759.8217 

   34000    2.0174621  0.057105551    2.0723261   0.64467755    4670.3864 

   35000    2.0063359  0.066058747    2.0701654   0.69838429    4569.2775 

   36000    2.0235751  0.051897263     2.073224   0.72690959    4489.1412 

   37000    1.9919056  0.082155679    2.0718481   0.76989663    4425.5319 

   38000    2.0165145  0.054900127    2.0691741   0.71506922    4363.1001 

   39000    1.9914799  0.086534981    2.0758021   0.72573846    4295.6077 

   40000     2.021673  0.056008458    2.0754352   0.79323316     4230.918 

   41000    1.9991577  0.079224104    2.0761605   0.82959064    4176.1378 

   42000    2.0345579  0.049727153    2.0820245   0.76689891    4104.6621 

   43000    2.0198238  0.065055122    2.0826347   0.76350704    4053.1909 

   44000    2.0317758  0.055399257    2.0849176   0.81303541    4004.6782 

   45000    1.9768996    0.1069946    2.0816976    1.0368321    3965.6941 

   46000    2.0239006  0.068426868    2.0900787   0.82654301    3917.9121 

   47000    1.9974829   0.09160171    2.0868652   0.98260215    3875.9397 

   48000    2.0075343  0.086776604    2.0920804    1.0407931    3838.6358 

   49000    2.0377514  0.056590997    2.0920782   0.83309295    3806.7174 

   50000    1.9745583    0.1268781    2.0992424    1.0900442    3755.5166 

Loop time of 14.0181 on 1 procs for 50000 steps with 900 atoms



Pair  time (%) = 7.4275 (52.9851)

Neigh time (%) = 1.43155 (10.2122)

Comm  time (%) = 0.323036 (2.30442)

Outpt time (%) = 0.34462 (2.4584)

Other time (%) = 4.49138 (32.0399)



Nlocal:    900 ave 900 max 900 min

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

Nghost:    541 ave 541 max 541 min

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

Neighs:    5974 ave 5974 max 5974 min

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



Total # of neighbors = 5974

Ave neighs/atom = 6.63778

Neighbor list builds = 2779

Dangerous builds = 0

examples/colloid/log.colloid.10Sep10.linux.4

0 → 100644
+120 −0
Original line number Diff line number Diff line 
LAMMPS (10 Sep 2010)

# Big colloid particles and small LJ particles



units		lj

atom_style	atomic

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 processor grid

create_atoms	1 box

Created 900 atoms



set		group all type/fraction 2 0.96 23984

  861 settings made for type/fraction



mass		1 9

mass		2 1



velocity	all create 1.44 87287 loop geom



# multi neighbor and comm for efficiency



neighbor	1 multi

neigh_modify	delay 0

communicate	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 200 dump.colloid



thermo_style	custom step temp epair etotal press vol

thermo		1000



timestep	0.005



run		50000

Memory usage per processor = 1.72729 Mbytes

Step Temp E_pair TotEng Press Volume 

       0         1.44 -2.2136534e-06    1.4383978  0.014383923        90000 

    1000    1.9558819 -0.00044998322    1.9532587   0.01784589     99146.35 

    2000    2.0558568  0.011295331    2.0648679  0.021858185    96654.425 

    3000    2.1809647 0.0091754217    2.1877168  0.031294876     68756.47 

    4000    2.1960934 0.0028186107    2.1964719  0.049318667    42974.984 

    5000    2.1463273   0.01274853     2.156691   0.07399494    28660.577 

    6000    2.1073954 0.0076740495    2.1127279    0.0976574     21544.21 

    7000    2.0843824 -0.0020103233    2.0800561   0.11035975     17791.25 

    8000    2.0722812 -0.0055341093    2.0644446    0.1258002    15497.017 

    9000    2.0522409 0.0093070316    2.0592676   0.15067871    13886.344 

   10000    2.0479022  0.010202901    2.0558297   0.17098883    12621.592 

   11000    2.0380647  0.022149294    2.0579495   0.21289456     11513.93 

   12000    2.0325651  0.026302255     2.056609   0.25050503    10615.642 

   13000    2.0331572  0.023671803      2.05457   0.25207081    9861.9599 

   14000    2.0342067  0.019413601    2.0513601   0.24041021    9216.2616 

   15000    2.0332615  0.022775757    2.0537781   0.28291892    8634.8141 

   16000    2.0329345  0.020980606    2.0516563   0.29807127    8155.8981 

   17000     2.039188  0.014286071    2.0512083   0.30687321    7746.2435 

   18000    2.0452159 0.0092634432    2.0522068   0.31683468     7396.277 

   19000    2.0158626  0.035217228      2.04884   0.36610312    7082.1419 

   20000    2.0284664  0.032953766    2.0591663   0.39281877    6770.9589 

   21000    2.0226606  0.035814093    2.0562273   0.39437998    6521.4776 

   22000    2.0130135  0.040365662    2.0511425   0.44121773    6325.4746 

   23000     2.015032   0.04394302    2.0567361   0.45044797    6110.0623 

   24000    2.0242073  0.035871997    2.0578302   0.45322663    5904.7342 

   25000    2.0270024  0.035017804     2.059768   0.49773835    5697.3918 

   26000     2.002438  0.059035413    2.0592485   0.51121477    5547.7333 

   27000    2.0161827  0.040874692    2.0548172   0.52409916    5428.5263 

   28000    2.0221465  0.040780109    2.0606798   0.52891624    5265.4809 

   29000    1.9909985  0.070412989    2.0591993   0.57485997    5105.1236 

   30000    1.9936857   0.06411566    2.0555861   0.60206458    5028.4694 

   31000    2.0360818  0.026357606    2.0601771   0.51359522    4964.9556 

   32000    2.0140985  0.055233213    2.0670939   0.63839514    4848.1212 

   33000    1.9837082   0.07873748    2.0602416   0.71715999    4765.2405 

   34000    1.9966603  0.069959523    2.0644013   0.71341915    4682.4238 

   35000    2.0117471  0.056956101     2.066468   0.67375821    4631.0618 

   36000    2.0176258  0.062029231    2.0774132   0.74425024    4524.0425 

   37000    2.0152405  0.064303766    2.0773051   0.68581066    4425.9873 

   38000    1.9985654  0.081975898    2.0783207    0.7704637    4345.3174 

   39000    1.9858687  0.087849129    2.0715113   0.77585184    4288.3463 

   40000    2.0206318   0.05532156    2.0737082   0.78638075    4244.9796 

   41000    2.0193318  0.062817577    2.0799057   0.78429167    4167.5733 

   42000    2.0092077  0.071029098    2.0780044    0.7768825    4116.8138 

   43000    2.0153309  0.067818727    2.0809104   0.74734758    4079.7086 

   44000    2.0195532  0.065247754     2.082557    0.9316374    4026.2843 

   45000    1.9802241   0.10409164    2.0821154   0.96663918    3998.3262 

   46000    1.9854496    0.1075189    2.0907625     1.021584    3927.3112 

   47000    2.0432354  0.054434623    2.0953998   0.87230417    3861.9993 

   48000    2.0013528  0.092780712    2.0919098   0.96849477    3817.8083 

   49000     1.983561   0.10735506    2.0887121    1.0283904    3787.8018 

   50000    2.0011289  0.094204701    2.0931101   0.99135562    3764.0292 

Loop time of 6.56245 on 4 procs for 50000 steps with 900 atoms



Pair  time (%) = 1.86456 (28.4126)

Neigh time (%) = 0.363108 (5.53311)

Comm  time (%) = 1.97777 (30.1376)

Outpt time (%) = 0.247797 (3.77598)

Other time (%) = 2.10922 (32.1408)



Nlocal:    225 ave 246 max 210 min

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

Nghost:    310.25 ave 330 max 296 min

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

Neighs:    1520.75 ave 1622 max 1353 min

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



Total # of neighbors = 6083

Ave neighs/atom = 6.75889

Neighbor list builds = 2794

Dangerous builds = 0

examples/comb/log.comb.Cu.10Sep10.linux.1

0 → 100644
+69 −0
Original line number Diff line number Diff line 
LAMMPS (10 Sep 2010)

# Pure Cu crystal, structure created by LAMMPS, qeq off



units		metal

atom_style	charge

dimension       3

boundary        p p p



lattice  	fcc 3.615

Lattice spacing in x,y,z = 3.615 3.615 3.615

region		box block 0 4 0 4 0 4

create_box	1 box

Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)

  1 by 1 by 1 processor grid

create_atoms	1 box

Created 256 atoms

mass		1 63.54



pair_style	comb

pair_coeff	* * ffield.comb Cu



neighbor	0.5 bin

neigh_modify	every 1 delay 1 check yes 



#dump		1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz

#dump_modify	1 append yes element Cu



fix		1 all nve

timestep        0.00020



thermo_style	custom step temp etotal pe evdwl ecoul press vol lx ly lz xz

thermo_modify	norm yes

velocity	all create 10.1 2398378

thermo	  	1

run  		10

Memory usage per processor = 2.4156 Mbytes

Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 

       0         10.1   -3.5063151   -3.5076155   -3.5076155            0    27.496055    3023.4645        14.46        14.46        14.46            0 

       1    10.099643   -3.5063151   -3.5076155   -3.5076155            0    27.512983    3023.4645        14.46        14.46        14.46            0 

       2    10.098572   -3.5063151   -3.5076153   -3.5076153            0    27.563765    3023.4645        14.46        14.46        14.46            0 

       3    10.096788   -3.5063151   -3.5076151   -3.5076151            0     27.64839    3023.4645        14.46        14.46        14.46            0 

       4    10.094291   -3.5063151   -3.5076148   -3.5076148            0    27.766843    3023.4645        14.46        14.46        14.46            0 

       5     10.09108   -3.5063151   -3.5076144   -3.5076144            0    27.919101    3023.4645        14.46        14.46        14.46            0 

       6    10.087158   -3.5063151   -3.5076139   -3.5076139            0    28.105138    3023.4645        14.46        14.46        14.46            0 

       7    10.082524   -3.5063151   -3.5076133   -3.5076133            0    28.324919    3023.4645        14.46        14.46        14.46            0 

       8    10.077179   -3.5063151   -3.5076126   -3.5076126            0    28.578403    3023.4645        14.46        14.46        14.46            0 

       9    10.071123   -3.5063151   -3.5076118   -3.5076118            0    28.865545    3023.4645        14.46        14.46        14.46            0 

      10     10.06436   -3.5063151   -3.5076109   -3.5076109            0    29.186292    3023.4645        14.46        14.46        14.46            0 

Loop time of 0.803072 on 1 procs for 10 steps with 256 atoms



Pair  time (%) = 0.802078 (99.8762)

Neigh time (%) = 0 (0)

Comm  time (%) = 0.000501871 (0.0624939)

Outpt time (%) = 0.000251532 (0.0313212)

Other time (%) = 0.000240564 (0.0299555)



Nlocal:    256 ave 256 max 256 min

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

Nghost:    4375 ave 4375 max 4375 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: 172544 ave 172544 max 172544 min

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



Total # of neighbors = 172544

Ave neighs/atom = 674

Neighbor list builds = 0

Dangerous builds = 0

examples/comb/log.comb.Cu.10Sep10.linux.4

0 → 100644
+69 −0
Original line number Diff line number Diff line 
LAMMPS (10 Sep 2010)

# Pure Cu crystal, structure created by LAMMPS, qeq off



units		metal

atom_style	charge

dimension       3

boundary        p p p



lattice  	fcc 3.615

Lattice spacing in x,y,z = 3.615 3.615 3.615

region		box block 0 4 0 4 0 4

create_box	1 box

Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)

  1 by 2 by 2 processor grid

create_atoms	1 box

Created 256 atoms

mass		1 63.54



pair_style	comb

pair_coeff	* * ffield.comb Cu



neighbor	0.5 bin

neigh_modify	every 1 delay 1 check yes 



#dump		1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz

#dump_modify	1 append yes element Cu



fix		1 all nve

timestep        0.00020



thermo_style	custom step temp etotal pe evdwl ecoul press vol lx ly lz xz

thermo_modify	norm yes

velocity	all create 10.1 2398378

thermo	  	1

run  		10

Memory usage per processor = 1.90928 Mbytes

Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 

       0         10.1   -3.5063151   -3.5076155   -3.5076155            0    27.496055    3023.4645        14.46        14.46        14.46            0 

       1    10.099638   -3.5063151   -3.5076155   -3.5076155            0    27.513531    3023.4645        14.46        14.46        14.46            0 

       2    10.098553   -3.5063151   -3.5076153   -3.5076153            0    27.565957    3023.4645        14.46        14.46        14.46            0 

       3    10.096744   -3.5063151   -3.5076151   -3.5076151            0    27.653322    3023.4645        14.46        14.46        14.46            0 

       4    10.094212   -3.5063151   -3.5076148   -3.5076148            0    27.775611    3023.4645        14.46        14.46        14.46            0 

       5    10.090958   -3.5063151   -3.5076144   -3.5076144            0    27.932801    3023.4645        14.46        14.46        14.46            0 

       6    10.086981   -3.5063151   -3.5076139   -3.5076139            0    28.124863    3023.4645        14.46        14.46        14.46            0 

       7    10.082283   -3.5063151   -3.5076132   -3.5076132            0    28.351761    3023.4645        14.46        14.46        14.46            0 

       8    10.076864   -3.5063151   -3.5076125   -3.5076125            0    28.613454    3023.4645        14.46        14.46        14.46            0 

       9    10.070725   -3.5063151   -3.5076118   -3.5076118            0    28.909893    3023.4645        14.46        14.46        14.46            0 

      10    10.063868   -3.5063151   -3.5076109   -3.5076109            0    29.241022    3023.4645        14.46        14.46        14.46            0 

Loop time of 0.205428 on 4 procs for 10 steps with 256 atoms



Pair  time (%) = 0.198618 (96.685)

Neigh time (%) = 0 (0)

Comm  time (%) = 0.00622982 (3.0326)

Outpt time (%) = 0.0003618 (0.17612)

Other time (%) = 0.000218272 (0.106252)



Nlocal:    64 ave 64 max 64 min

Histogram: 4 0 0 0 0 0 0 0 0 0

Nghost:    2971 ave 2971 max 2971 min

Histogram: 4 0 0 0 0 0 0 0 0 0

Neighs:    0 ave 0 max 0 min

Histogram: 4 0 0 0 0 0 0 0 0 0

FullNghs: 43136 ave 43136 max 43136 min

Histogram: 4 0 0 0 0 0 0 0 0 0



Total # of neighbors = 172544

Ave neighs/atom = 674

Neighbor list builds = 0

Dangerous builds = 0

examples/comb/log.comb.Cu2O.elastic.10Sep10.linux.1

0 → 100644
+327 −0

File added.

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