Commit daf71947 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15771 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent fdd61cf3

examples/DIFFUSE/log.13Oct16.msd.2d.g++.8

0 → 100644
+245 −0
Original line number Diff line number Diff line 
LAMMPS (13 Oct 2016)

# sample LAMMPS input script for diffusion of 2d LJ liquid

# mean-squared displacement via compute msd



# settings



variable	x equal 40

variable	y equal 40



variable	rho equal 0.6

variable        t equal 1.0

variable	rc equal 2.5



# problem setup



units		lj

dimension	2

atom_style	atomic

neigh_modify	delay 0 every 1



lattice         sq2 ${rho}

lattice         sq2 0.6

Lattice spacing in x,y,z = 1.82574 1.82574 1.82574

region          simbox block 0 $x 0 $y -0.1 0.1

region          simbox block 0 40 0 $y -0.1 0.1

region          simbox block 0 40 0 40 -0.1 0.1

create_box      1 simbox

Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)

  4 by 2 by 1 MPI processor grid

create_atoms    1 box

Created 3200 atoms



pair_style      lj/cut ${rc}

pair_style      lj/cut 2.5

pair_coeff      * * 1 1



mass            * 1.0

velocity        all create $t 97287

velocity        all create 1 97287



fix             1 all nve

fix	        2 all langevin $t $t 0.1 498094

fix	        2 all langevin 1 $t 0.1 498094

fix	        2 all langevin 1 1 0.1 498094

fix	        3 all enforce2d



# equilibration run



thermo          1000

run	        5000

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 = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4 -> bins = 53 53 1

Memory usage per processor = 2.478 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0            1     -1.56492            0   -0.5652325   -1.5346995 

    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 

    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 

    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 

    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 

    5000   0.97069905   -1.5851114            0  -0.61471567   0.90108287 

Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms



Performance: 3896017.421 tau/day, 9018.559 timesteps/s

98.9% CPU use with 8 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.23992    | 0.24608    | 0.25161    |   0.7 | 44.39

Neigh   | 0.063106   | 0.064417   | 0.066279   |   0.4 | 11.62

Comm    | 0.072465   | 0.085066   | 0.094837   |   2.3 | 15.34

Output  | 0.00013208 | 0.00013691 | 0.00014591 |   0.0 |  0.02

Modify  | 0.11441    | 0.11621    | 0.11769    |   0.3 | 20.96

Other   |            | 0.04251    |            |       |  7.67



Nlocal:    400 ave 406 max 394 min

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

Nghost:    202.5 ave 212 max 191 min

Histogram: 1 0 0 0 3 1 0 2 0 1

Neighs:    2800.88 ave 2903 max 2690 min

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



Total # of neighbors = 22407

Ave neighs/atom = 7.00219

Neighbor list builds = 599

Dangerous builds = 0



unfix		2



# data gathering run



reset_timestep  0



# factor of 4 in 2 variables is for 2d



compute         msd all msd com yes

variable        twopoint equal c_msd[4]/4/(step*dt+1.0e-6)

fix             9 all vector 10 c_msd[4]

variable        fitslope equal slope(f_9)/4/(10*dt)



thermo_style	custom step temp c_msd[4] v_twopoint v_fitslope



# only need to run for 10K steps to make a good 100-frame movie



#dump	        1 all custom 1 tmp.dump id type vx vy vz



#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2



thermo          1000

run	        100000

Memory usage per processor = 2.853 Mbytes

Step Temp c_msd[4] v_twopoint v_fitslope 

       0   0.97069905            0            0        5e+20 

    1000   0.98138076    4.0484996   0.20242494   0.18046446 

    2000   0.97606079    9.2121392   0.23030346    0.2091528 

    3000   0.97924866    14.815034   0.24691721   0.22619184 

    4000   0.98568451    20.516817   0.25646019   0.23715506 

    5000   0.97551815     27.33922   0.27339219   0.24709999 

    6000   0.98482252     34.37734   0.28647782   0.25735178 

    7000    0.9672559    41.696689   0.29783348   0.26654059 

    8000    0.9836541    48.340277   0.30212673   0.27440308 

    9000   0.99087147    56.042692   0.31134828   0.28113047 

   10000   0.99663166     63.69663   0.31848314   0.28767921 

   11000   0.97776688    71.144109   0.32338231   0.29344527 

   12000   0.98246011    78.301774   0.32625739   0.29849471 

   13000   0.98788732    85.061923   0.32716124    0.3026655 

   14000   0.96872483      91.1658   0.32559214   0.30601023 

   15000   0.98955796    97.278388   0.32426129    0.3084275 

   16000   0.99855196    104.23997    0.3257499   0.31049883 

   17000   0.98600861    110.66055    0.3254722   0.31220348 

   18000   0.98696963    116.90111   0.32472531   0.31352676 

   19000    0.9881192    124.21305   0.32687644   0.31480062 

   20000   0.98527319    131.09874   0.32774685   0.31596198 

   21000   0.99015191    137.89263   0.32831579   0.31705324 

   22000   0.97972418    146.68982   0.33338595   0.31833889 

   23000   0.98911012     155.1264   0.33723129   0.31979515 

   24000   0.98810498    162.88634   0.33934653   0.32131187 

   25000   0.96961962    170.37907   0.34075814   0.32276215 

   26000   0.99118408    179.26511   0.34474059   0.32427111 

   27000   0.98515159    185.90764    0.3442734   0.32574529 

   28000   0.98951677    192.12183   0.34307469   0.32700292 

   29000    0.9832026    196.99457   0.33964581   0.32799023 

   30000   0.98449493    203.48475   0.33914124    0.3287171 

   31000   0.96585993    210.06193   0.33880956   0.32935775 

   32000   0.98758117    218.94174   0.34209646   0.33001591 

   33000   0.98875584    225.96489   0.34237104   0.33072947 

   34000   0.98007229     233.5792   0.34349882    0.3314385 

   35000   0.98415295    241.98148   0.34568783   0.33216634 

   36000   0.98101154    250.30876   0.34765106   0.33295272 

   37000   0.97606878     258.2127   0.34893608   0.33377673 

   38000   0.97220293    266.40464   0.35053242   0.33459273 

   39000     0.979783     272.8578   0.34981769   0.33539728 

   40000   0.98375673    279.87598   0.34984497   0.33609699 

   41000   0.97506523    288.07676   0.35131312   0.33677708 

   42000   0.97106749    296.11647    0.3525196   0.33751312 

   43000   0.97717259    304.46747   0.35403194   0.33823441 

   44000   0.98541435    312.57228   0.35519578    0.3389771 

   45000   0.97678287    321.82674   0.35758527   0.33973306 

   46000   0.98169719    329.78197   0.35845866   0.34051748 

   47000   0.99471466    337.11283   0.35863066   0.34127239 

   48000   0.98332437     346.0754    0.3604952   0.34202442 

   49000   0.98126947    356.11859   0.36338631   0.34282132 

   50000   0.98809751    365.65248   0.36565248   0.34368171 

   51000   0.95919516    373.91833   0.36658659   0.34454516 

   52000   0.98097913    381.26492   0.36660089   0.34538506 

   53000   0.97774072    388.81031   0.36680218   0.34618232 

   54000   0.99096915    395.56767   0.36626636    0.3469296 

   55000   0.97652739    401.72735   0.36520668   0.34760374 

   56000   0.99185306    407.28834    0.3636503   0.34819906 

   57000   0.96289342    414.75298    0.3638184   0.34871992 

   58000   0.97871716    424.69443   0.36611588   0.34927986 

   59000   0.98637393    433.14205   0.36706953   0.34986296 

   60000   0.98009845    438.14533   0.36512111   0.35040349 

   61000   0.99416712    446.08007    0.3656394   0.35088379 

   62000   0.97612483    450.90846   0.36363585   0.35132647 

   63000   0.97786531    455.36749   0.36140277   0.35167458 

   64000   0.99080668    458.04873   0.35785057    0.3519105 

   65000   0.97952497    461.31241    0.3548557    0.3520506 

   66000   0.98095955    463.91727   0.35145248   0.35207764 

   67000   0.98370788       468.93   0.34994776   0.35204043 

   68000   0.96931818    471.07765   0.34638063   0.35192685 

   69000   0.98512552    474.59146   0.34390685   0.35174053 

   70000   0.98065743    478.66071    0.3419005   0.35149002 

   71000   0.98971283    482.57357   0.33984054   0.35119434 

   72000   0.99890324    485.32018    0.3370279   0.35084345 

   73000   0.98649924    490.19497   0.33574998   0.35043722 

   74000   0.98723422    496.04991   0.33516886   0.35003351 

   75000    1.0025633     501.6313   0.33442087   0.34962094 

   76000   0.97859959    505.97813   0.33288035   0.34921013 

   77000   0.97973006    510.55334   0.33152814    0.3487692 

   78000    0.9903944    515.06966   0.33017286   0.34830833 

   79000   0.96847518    518.76483   0.32833217    0.3478214 

   80000   0.99171112    524.18127   0.32761329   0.34733349 

   81000   0.97202573    529.09959   0.32660468    0.3468315 

   82000   0.99368438    535.80271   0.32670897   0.34633058 

   83000   0.97932483    543.08233   0.32715803   0.34586259 

   84000   0.99078651    547.57861   0.32593965   0.34540839 

   85000   0.98973457    552.24581   0.32485048   0.34493584 

   86000    0.9835873     557.3493   0.32404029   0.34446152 

   87000   0.97180564    564.93434   0.32467491   0.34400358 

   88000   0.99743353    571.39837   0.32465817    0.3435667 

   89000   0.98993437    577.81703   0.32461631    0.3431411 

   90000    0.9926071    583.39378   0.32410765     0.342724 

   91000   0.98800458    591.08741    0.3247733   0.34232767 

   92000   0.98501879    596.10133   0.32396811   0.34193949 

   93000   0.98810082    604.02652   0.32474544    0.3415681 

   94000   0.97563748    609.43676   0.32416849     0.341209 

   95000   0.97283448    615.15754   0.32376713   0.34084828 

   96000    0.9883071    622.30912   0.32411933   0.34049871 

   97000   0.97717678    628.84457   0.32414669   0.34016355 

   98000   0.97190208    634.37377   0.32366009    0.3398341 

   99000   0.98687379    640.66666   0.32356902   0.33950845 

  100000   0.97559757    646.96406   0.32348203   0.33919036 

Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms



Performance: 4505729.040 tau/day, 10429.928 timesteps/s

99.4% CPU use with 8 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 4.8572     | 4.9363     | 4.9822     |   1.7 | 51.49

Neigh   | 1.3583     | 1.376      | 1.3991     |   1.2 | 14.35

Comm    | 1.5192     | 1.7079     | 1.8264     |   7.2 | 17.81

Output  | 0.0085125  | 0.0086059  | 0.0089455  |   0.1 |  0.09

Modify  | 0.77663    | 0.7903     | 0.81378    |   1.3 |  8.24

Other   |            | 0.7686     |            |       |  8.02



Nlocal:    400 ave 413 max 391 min

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

Nghost:    204.75 ave 213 max 197 min

Histogram: 1 1 0 1 0 3 0 1 0 1

Neighs:    2800.62 ave 2959 max 2661 min

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



Total # of neighbors = 22405

Ave neighs/atom = 7.00156

Neighbor list builds = 12728

Dangerous builds = 0

Total wall time: 0:00:10

examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8

0 → 100644
+246 −0
Original line number Diff line number Diff line 
LAMMPS (13 Oct 2016)

# sample LAMMPS input script for diffusion of 2d LJ liquid

# mean-squared displacement via compute msd



# settings



variable	x equal 40

variable	y equal 40



variable	rho equal 0.6

variable        t equal 1.0

variable	rc equal 2.5



# problem setup



units		lj

dimension	2

atom_style	atomic

neigh_modify	delay 0 every 1



lattice         sq2 ${rho}

lattice         sq2 0.6

Lattice spacing in x,y,z = 1.82574 1.82574 1.82574

region          simbox block 0 $x 0 $y -0.1 0.1

region          simbox block 0 40 0 $y -0.1 0.1

region          simbox block 0 40 0 40 -0.1 0.1

create_box      1 simbox

Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)

  4 by 2 by 1 MPI processor grid

create_atoms    1 box

Created 3200 atoms



pair_style      lj/cut ${rc}

pair_style      lj/cut 2.5

pair_coeff      * * 1 1



mass            * 1.0

velocity        all create $t 97287

velocity        all create 1 97287



fix             1 all nve

fix	        2 all langevin $t $t 0.1 498094

fix	        2 all langevin 1 $t 0.1 498094

fix	        2 all langevin 1 1 0.1 498094

fix	        3 all enforce2d



# equilibration run



thermo          1000

run	        5000

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 = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4 -> bins = 53 53 1

Memory usage per processor = 2.478 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0            1     -1.56492            0   -0.5652325   -1.5346995 

    1000   0.97537833   -1.5723957            0   -0.5973222   0.92877783 

    2000   0.99008371   -1.5748206            0  -0.58504633    1.0809416 

    3000    1.0111412   -1.5848987            0  -0.57407352    1.0174297 

    4000    1.0055417   -1.5857581            0  -0.58053054   0.95647691 

    5000   0.97069905   -1.5851114            0  -0.61471567   0.90108287 

Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms



Performance: 3873826.669 tau/day, 8967.191 timesteps/s

99.1% CPU use with 8 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.23784    | 0.24683    | 0.25594    |   1.0 | 44.27

Neigh   | 0.062975   | 0.06439    | 0.0662     |   0.4 | 11.55

Comm    | 0.083826   | 0.092564   | 0.1035     |   2.1 | 16.60

Output  | 0.00011778 | 0.00012615 | 0.00014257 |   0.1 |  0.02

Modify  | 0.11466    | 0.11648    | 0.1187     |   0.4 | 20.89

Other   |            | 0.0372     |            |       |  6.67



Nlocal:    400 ave 406 max 394 min

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

Nghost:    202.5 ave 212 max 191 min

Histogram: 1 0 0 0 3 1 0 2 0 1

Neighs:    2800.88 ave 2903 max 2690 min

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



Total # of neighbors = 22407

Ave neighs/atom = 7.00219

Neighbor list builds = 599

Dangerous builds = 0



unfix		2



# data gathering run



reset_timestep  0



compute         vacf all vacf

fix             4 all ave/time 1 1 1 c_vacf[4] #file tmp.vacf



# factor of 0.5 is for 2d



fix             5 all vector 1 c_vacf[4]

variable        vacf equal 0.5*dt*trap(f_5)



thermo_style	custom step temp c_vacf[4] v_vacf



# only need to run for 10K steps to make a good 100-frame movie



#dump	        1 all custom 1 tmp.dump id type vx vy vz



#dump		2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2



thermo          1000

run	        100000

Memory usage per processor = 2.853 Mbytes

Step Temp c_vacf[4] v_vacf 

       0   0.97069905    1.9407914            0 

    1000   0.98138076  0.029239763   0.22157396 

    2000   0.97606079 -0.0015179052   0.23974121 

    3000   0.97924866 -0.013873067   0.21877575 

    4000   0.98568451  0.026969065   0.24052934 

    5000   0.97551815  0.050232557   0.24508207 

    6000   0.98482252 -0.0018424259   0.25686293 

    7000    0.9672559  0.018499957   0.27279836 

    8000    0.9836541 -0.022683127   0.27022734 

    9000   0.99087147 0.0071767632   0.25267902 

   10000   0.99663166 -0.011971734    0.2645822 

   11000   0.97776688   0.01601675   0.27801788 

   12000   0.98246011 0.0085456779   0.29207728 

   13000   0.98788732 0.0054252587   0.29148533 

   14000   0.96872483 0.0087976064   0.29645689 

   15000   0.98955796 -0.060068996   0.28904116 

   16000   0.99855196 -0.0066979853   0.24964957 

   17000   0.98600861  0.021334454   0.23410452 

   18000   0.98696963  -0.01971883   0.23190572 

   19000    0.9881192 -0.022828159   0.20882183 

   20000   0.98527319 -0.0085783561   0.20610922 

   21000   0.99015191 -0.0061019744   0.20199693 

   22000   0.97972418  -0.04380952   0.22099864 

   23000   0.98911012 -0.0031381071   0.19304223 

   24000   0.98810498  0.023131507   0.18483784 

   25000   0.96961962 -0.020892151   0.17128259 

   26000   0.99118408   0.02918818   0.15353531 

   27000   0.98515159 -0.026417648    0.1457756 

   28000   0.98951677  0.010372147   0.13321212 

   29000    0.9832026 0.00058150905   0.13262151 

   30000   0.98449493 0.0012256712   0.13576655 

   31000   0.96585993 0.0053021384   0.10734708 

   32000   0.98758117 -0.011513109   0.11473375 

   33000   0.98875584 -0.0089140499   0.13003947 

   34000   0.98007229  0.023423116     0.145185 

   35000   0.98415295 -0.0078343607   0.16513809 

   36000   0.98101154  0.025471963    0.1296799 

   37000   0.97606878 -0.016931612   0.11515595 

   38000   0.97220293 -0.015288346   0.12046935 

   39000     0.979783  0.039556949   0.10596988 

   40000   0.98375673 0.0098704124   0.15651085 

   41000   0.97506523 -0.029457701   0.14822207 

   42000   0.97106749 -0.024867475   0.12266294 

   43000   0.97717259  0.010866403   0.14228602 

   44000   0.98541435 -0.031545234   0.13017093 

   45000   0.97678287 -0.011024372   0.11824999 

   46000   0.98169719  0.011925437    0.1390346 

   47000   0.99471466 0.0048178625   0.13076123 

   48000   0.98332437  0.045576305   0.12667585 

   49000   0.98126947 -0.044123768   0.13582991 

   50000   0.98809751  0.014296599   0.12323107 

   51000   0.95919516 -0.0091171161    0.1494511 

   52000   0.98097913  0.010081012   0.12805794 

   53000   0.97774072  0.043349117   0.14524942 

   54000   0.99096915  0.021179196    0.1355801 

   55000   0.97652739 -0.015118967   0.14955035 

   56000   0.99185306 0.0018045061   0.16706629 

   57000   0.96289342 0.0095090659   0.19215008 

   58000   0.97871716 -0.028989119   0.20370326 

   59000   0.98637393 0.0067841088   0.21820001 

   60000   0.98009845  0.011559251   0.24504916 

   61000   0.99416712 0.0099372548   0.24882366 

   62000   0.97612483  0.014677063   0.25146482 

   63000   0.97786531 -0.0047938112   0.26052305 

   64000   0.99080668  -0.01632121   0.24744267 

   65000   0.97952497 0.0070583633   0.22323997 

   66000   0.98095955  0.036296232    0.2151706 

   67000   0.98370788 -0.0040313363   0.22236193 

   68000   0.96931818    0.0231486   0.20397659 

   69000   0.98512552 -0.017450997   0.21854935 

   70000   0.98065743  0.046916694    0.2080453 

   71000   0.98971283  0.010974871   0.21628306 

   72000   0.99890324 -0.023780184   0.23385876 

   73000   0.98649924  0.012862733   0.23458964 

   74000   0.98723422 -0.0096252165   0.23873216 

   75000    1.0025633 -0.070387674    0.2275029 

   76000   0.97859959 0.0058897922   0.22954358 

   77000   0.97973006 -0.0082868083   0.25189797 

   78000    0.9903944 -0.042368536   0.26564349 

   79000   0.96847518 -0.050630573   0.25344248 

   80000   0.99171112  0.012126001   0.23257751 

   81000   0.97202573 -0.029816198   0.27354387 

   82000   0.99368438  0.030082951   0.27859495 

   83000   0.97932483 -0.0081664387   0.27409123 

   84000   0.99078651  0.056610231   0.27593659 

   85000   0.98973457  0.020424285   0.31002605 

   86000    0.9835873 -0.0016980943   0.30158255 

   87000   0.97180564 -0.0051924508   0.27401969 

   88000   0.99743353 -0.030700753   0.24105471 

   89000   0.98993437 0.0087866525   0.23913724 

   90000    0.9926071 -0.014023378   0.24202489 

   91000   0.98800458  0.033613695    0.2238248 

   92000   0.98501879   -0.0406599   0.21809043 

   93000   0.98810082  0.027637634   0.21550897 

   94000   0.97563748 0.0014112208   0.18954766 

   95000   0.97283448 0.0093796591   0.17838358 

   96000    0.9883071  0.033049994   0.18594703 

   97000   0.97717678   0.01070451   0.19203994 

   98000   0.97190208  0.015065013   0.20906937 

   99000   0.98687379 -0.036869401   0.22993959 

  100000   0.97559757  0.045464091   0.23369283 

Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms



Performance: 3987213.825 tau/day, 9229.662 timesteps/s

99.5% CPU use with 8 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 4.8486     | 4.9469     | 5.0248     |   2.8 | 45.66

Neigh   | 1.3613     | 1.374      | 1.3916     |   0.8 | 12.68

Comm    | 1.8181     | 1.9534     | 2.0665     |   5.7 | 18.03

Output  | 0.016565   | 0.016701   | 0.017039   |   0.1 |  0.15

Modify  | 1.8395     | 1.9053     | 1.9704     |   2.8 | 17.59

Other   |            | 0.6383     |            |       |  5.89



Nlocal:    400 ave 413 max 391 min

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

Nghost:    204.75 ave 213 max 197 min

Histogram: 1 1 0 1 0 3 0 1 0 1

Neighs:    2800.62 ave 2959 max 2661 min

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



Total # of neighbors = 22405

Ave neighs/atom = 7.00156

Neighbor list builds = 12728

Dangerous builds = 0

Total wall time: 0:00:11

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