Commit 64f14417 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4711 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 8de360ff

examples/colloid/log.colloid.15Jan10.linux.1

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Original line number Diff line number Diff line 
LAMMPS (15 Jan 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0

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    1.7234872 0.00099573088     1.722568  0.015516409    101033.02 

    2000    1.9974361 0.0027373053    1.9979541  0.018869215    99044.293 

    3000     2.116115 0.0064857798    2.1202495  0.029970575    68999.265 

    4000    2.0978894 0.0081401736    2.1036985  0.049192217    41664.559 

    5000    2.0428684 -0.00010722124    2.0404914  0.069391752    27239.613 

    6000    2.0019359 0.0031628998    2.0028745  0.094013179    20369.423 

    7000    1.9859909 0.0083584854    1.9921427   0.11907545    16950.719 

    8000    1.9844995  0.018823846    2.0011183   0.15140382    14935.157 

    9000    2.0136412 0.0025888284    2.0139927    0.1508535    13559.132 

   10000     2.024979 -0.0013617278    2.0213673   0.15704325    12420.294 

   11000    2.0057261  0.014666062    2.0181636   0.19581308    11367.173 

   12000    1.9956708  0.027177644    2.0206311   0.21321459     10459.36 

   13000     1.997959  0.021344943    2.0170839   0.22767396    9688.7235 

   14000    2.0053139  0.018752845    2.0218386   0.23937083    9035.5752 

   15000    2.0080175  0.016121788    2.0219082   0.27453929    8472.6599 

   16000    2.0134958  0.017190654    2.0284492   0.29545011    8018.8828 

   17000    1.9948094  0.030593329    2.0231862   0.31639324    7660.0205 

   18000    1.9888692   0.03866718    2.0253265   0.37624499    7343.9859 

   19000    2.0178864  0.015784628    2.0314289   0.36208151     7023.858 

   20000    1.9974336  0.034034531    2.0292487   0.36977001    6766.9639 

   21000    2.0075467  0.027457169    2.0327733   0.39171127    6515.3658 

   22000    1.9776525  0.056409217    2.0318644   0.45665965    6308.0579 

   23000    1.9868859   0.05125969     2.035938   0.45997816    6086.0284 

   24000     2.025575  0.024864929    2.0481893    0.4614688    5877.2914 

   25000    2.0229719   0.02993936    2.0506635   0.43975465    5678.5742 

   26000    2.0116839  0.040441814    2.0498905   0.56364223    5510.9392 

   27000    1.9927671  0.056780401    2.0473333    0.5435277    5418.0519 

   28000    2.0002455  0.048430948    2.0464539   0.54245177    5293.9817 

   29000    2.0027552  0.045188838    2.0457187   0.59393189    5149.2915 

   30000    2.0110981   0.04212224    2.0509858   0.53983977    5024.1603 

   31000    2.0103074  0.040614839    2.0486886   0.59127674    4968.3476 

   32000    2.0131878  0.034850997    2.0458019   0.54445776    4887.6392 

   33000    1.9795396   0.06888144    2.0462216   0.65710066    4759.8655 

   34000    2.0089206  0.044451973    2.0511405   0.61216346    4649.6158 

   35000    1.9852871  0.070975603    2.0540568   0.67074703    4575.8914 

   36000    1.9955339  0.069823373      2.06314    0.6720079    4498.8166 

   37000    2.0204607  0.039300432    2.0575161   0.60707297    4445.1332 

   38000    2.0066321  0.049640648    2.0540432   0.67871134    4366.3923 

   39000    1.9985924  0.072532872    2.0689046   0.77767565    4275.8245 

   40000    1.9910609  0.092339589    2.0811882   0.87608554    4203.2838 

   41000    1.9860042   0.10022021    2.0840177   0.86512783     4157.403 

   42000    2.0155072  0.068809689    2.0820775   0.80227153    4104.6347 

   43000    1.9766433  0.098409454    2.0728565   0.90326816    4041.9332 

   44000    1.9849649  0.075124531    2.0578839   0.90303861    3977.2148 

   45000     2.016926  0.053835025      2.06852   0.93357872    3939.6486 

   46000    2.0139764  0.062641204    2.0743798   0.92342056     3885.512 

   47000      2.00577   0.07951429    2.0830556   0.91383738    3864.1237 

   48000    2.0129787  0.091650954     2.102393   0.87567088    3815.2512 

   49000    2.0113794  0.085651277    2.0947959    0.8792936    3790.0177 

   50000    2.0081683  0.088519221    2.0944563   0.96671733    3739.3343 

Loop time of 12.9281 on 1 procs for 50000 steps with 900 atoms



Pair  time (%) = 7.46432 (57.7373)

Neigh time (%) = 1.48375 (11.477)

Comm  time (%) = 0.328302 (2.53945)

Outpt time (%) = 0.343754 (2.65898)

Other time (%) = 3.30794 (25.5873)



Nlocal:    900 ave 900 max 900 min

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

Nghost:    604 ave 604 max 604 min

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

Neighs:    6045 ave 6045 max 6045 min

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



Total # of neighbors = 6045

Ave neighs/atom = 6.71667

Neighbor list builds = 2774

Dangerous builds = 0

examples/colloid/log.colloid.15Jan10.linux.4

deleted100644 → 0
+0 −120
Original line number Diff line number Diff line 
LAMMPS (15 Jan 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0

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    1.7234872 0.00099573088     1.722568  0.015516409    101033.02 

    2000    1.9974361 0.0027373053    1.9979541  0.018869215    99044.293 

    3000     2.116115 0.0064857798    2.1202495  0.029970575    68999.265 

    4000    2.0978894 0.0081401738    2.1036985  0.049192217    41664.559 

    5000    2.0428684 -0.00010721686    2.0404914  0.069391753    27239.613 

    6000    2.0019422 0.0031508864    2.0028687  0.094008052     20369.42 

    7000    1.9804962  0.014232286    1.9925279    0.1213326    16950.471 

    8000    1.9799939   0.02110424    1.9988982   0.14355161    14946.998 

    9000    2.0086754 0.0075582088    2.0140018   0.15413456    13541.773 

   10000    2.0111846  0.014837261    2.0237872   0.17815644    12376.563 

   11000    2.0009867  0.023585324    2.0223487   0.18476862    11349.094 

   12000    2.0081888  0.021042968    2.0270005   0.20805315    10413.786 

   13000    2.0073242  0.022660628    2.0277545    0.2618024    9580.8617 

   14000    2.0132995  0.011098412    2.0221609   0.24241844    8955.2796 

   15000    1.9935123  0.027506763     2.018804   0.28347963    8481.1002 

   16000    2.0138701  0.010098081    2.0217306   0.27116735    8101.8048 

   17000    1.9961144  0.032341929    2.0262384   0.35173752    7726.2016 

   18000    2.0062141  0.017727613    2.0217126   0.31815455    7335.2691 

   19000    1.9722426  0.049842571    2.0198938   0.38305016    7017.8694 

   20000    2.0105249  0.025718126    2.0340091   0.39144988    6741.2107 

   21000    2.0202359  0.021844017    2.0398352   0.37267453    6490.7505 

   22000    2.0170475  0.027363384    2.0421698    0.3980519    6260.4648 

   23000    2.0002266  0.044664532    2.0426686   0.46416007    6036.0867 

   24000    2.0244857  0.018602855    2.0408391   0.44083256    5860.8857 

   25000    2.0155484  0.026604773    2.0399137   0.45089025    5705.4285 

   26000    2.0042083  0.038741004    2.0407225   0.50867855    5561.0521 

   27000    1.9890793    0.0499586    2.0368278   0.50693757    5431.3526 

   28000    2.0218464   0.03042568    2.0500256   0.50915338    5263.3705 

   29000    1.9873046  0.070059134    2.0551556   0.61561587    5138.5563 

   30000    2.0292021  0.023123832    2.0500712   0.56287385     5021.227 

   31000    1.9989274  0.056386862    2.0530932   0.62191836    4892.4219 

   32000    1.9785651  0.069403334      2.04577    0.6742955    4820.7949 

   33000    1.9876977  0.072553911    2.0580431   0.70765298    4749.2349 

   34000    1.9947836   0.07320354    2.0657708   0.70095294    4667.4497 

   35000    2.0136399  0.058792128    2.0701947   0.70766639    4572.4829 

   36000    2.0168328  0.054366679    2.0689586   0.72746701     4465.383 

   37000    2.0156725  0.058393266    2.0718261   0.67356394    4423.8328 

   38000    2.0069983  0.063326137    2.0680945   0.69973651    4367.1573 

   39000    1.9848816  0.069121229    2.0517974    0.8203791     4284.988 

   40000    2.0023359  0.060995146    2.0611062   0.79316005    4178.2125 

   41000     1.993631  0.070869533    2.0622854   0.83534613    4125.4539 

   42000    1.9734126  0.092315085     2.063535   0.90817003    4122.7493 

   43000    1.9855237  0.090960071    2.0742776   0.85735304    4071.5294 

   44000    2.0136311  0.069947968    2.0813417   0.84905758    3994.5619 

   45000    2.0118382  0.068803927    2.0784067   0.80982528    3931.1881 

   46000    2.0567836  0.034733386    2.0892317   0.82276486     3901.416 

   47000     1.990275  0.091141439     2.079205    0.9321676    3851.0061 

   48000    2.0059895  0.081535957    2.0852966    0.8686178    3826.0905 

   49000    2.0276188  0.060350089     2.085716   0.89407727     3786.439 

   50000    2.0129898    0.0842833    2.0950365   0.98615893    3740.8972 

Loop time of 28.5106 on 4 procs for 50000 steps with 900 atoms



Pair  time (%) = 2.29112 (8.03604)

Neigh time (%) = 0.42835 (1.50242)

Comm  time (%) = 14.4108 (50.5454)

Outpt time (%) = 0.368388 (1.29211)

Other time (%) = 11.0119 (38.624)



Nlocal:    225 ave 245 max 205 min

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

Nghost:    310.5 ave 320 max 292 min

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

Neighs:    1501 ave 1612 max 1344 min

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



Total # of neighbors = 6004

Ave neighs/atom = 6.67111

Neighbor list builds = 2778

Dangerous builds = 0

examples/comb/log.comb.Cu.15Jan10.linux.1

deleted100644 → 0
+0 −69
Original line number Diff line number Diff line 
LAMMPS (3 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 = 2.55348 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 0.799183 on 1 procs for 10 steps with 256 atoms



Pair  time (%) = 0.79663 (99.6805)

Neigh time (%) = 0 (0)

Comm  time (%) = 0.000517845 (0.0647968)

Outpt time (%) = 0.00177693 (0.222344)

Other time (%) = 0.000258446 (0.0323387)



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.15Jan10.linux.4

deleted100644 → 0
+0 −69
Original line number Diff line number Diff line 
LAMMPS (3 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 = 2.02958 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 0.203218 on 4 procs for 10 steps with 256 atoms



Pair  time (%) = 0.197568 (97.2197)

Neigh time (%) = 0 (0)

Comm  time (%) = 0.00359905 (1.77103)

Outpt time (%) = 0.00184023 (0.905546)

Other time (%) = 0.000210822 (0.103742)



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.15Jan10.linux.1

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