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2016-02-15 18:06:11 +00:00
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LAMMPS (15 Feb 2016)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.17878 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
Loop time of 1.034 on 1 procs for 2000 steps with 400 atoms
Performance: 334235.078 tau/day, 1934.231 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.82535 | 0.82535 | 0.82535 | 0.0 | 79.82
Neigh | 0.01368 | 0.01368 | 0.01368 | 0.0 | 1.32
Comm | 0.011166 | 0.011166 | 0.011166 | 0.0 | 1.08
Output | 0.00032282 | 0.00032282 | 0.00032282 | 0.0 | 0.03
Modify | 0.17955 | 0.17955 | 0.17955 | 0.0 | 17.36
Other | | 0.003941 | | | 0.38
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 249 ave 249 max 249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3031 ave 3031 max 3031 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3031
Ave neighs/atom = 7.5775
Neighbor list builds = 140
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.18892 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
2100 2.0067383 -3.4164295 -1.402453 0.63163512 1121.7026
2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
2300 2.0418707 -3.4552616 -1.4277716 0.58834236 1121.7026
2400 2.0126621 -3.424202 -1.3839096 0.80723942 1121.7026
2500 1.9403964 -3.3489489 -1.3995215 0.79492719 1121.7026
2600 2.0459304 -3.4600931 -1.4229608 0.69699402 1121.7026
2700 2.0032293 -3.4126492 -1.429784 0.44210814 1121.7026
2800 1.9367905 -3.345688 -1.4171068 0.6872734 1121.7026
2900 1.9870908 -3.3983385 -1.4218501 0.42402247 1121.7026
3000 1.9654849 -3.3767671 -1.3835149 0.6611643 1121.7026
3100 1.9308462 -3.3343018 -1.3895992 0.45213534 1121.7026
3200 1.8924656 -3.2956948 -1.4157919 0.56524685 1121.7026
3300 1.8802888 -3.2822198 -1.4071878 0.86030365 1121.7026
3400 1.8847013 -3.2852796 -1.4162404 0.91660541 1121.7026
3500 1.9290452 -3.3332356 -1.3889879 0.70770119 1121.7026
3600 1.9223314 -3.32413 -1.3896278 0.56763748 1121.7026
3700 1.9185132 -3.3197222 -1.3913701 0.66889312 1121.7026
3800 1.877321 -3.2796045 -1.4050964 0.67335591 1121.7026
3900 1.9250447 -3.3313033 -1.3872185 0.64573122 1121.7026
4000 1.8574113 -3.2592142 -1.3807543 0.46117918 1121.7026
Loop time of 1.15469 on 1 procs for 2000 steps with 400 atoms
Performance: 299301.907 tau/day, 1732.071 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 | 1.0251 | 1.0251 | 1.0251 | 0.0 | 88.77
Neigh | 0.0063124 | 0.0063124 | 0.0063124 | 0.0 | 0.55
Comm | 0.011792 | 0.011792 | 0.011792 | 0.0 | 1.02
Output | 0.00035834 | 0.00035834 | 0.00035834 | 0.0 | 0.03
Modify | 0.10537 | 0.10537 | 0.10537 | 0.0 | 9.13
Other | | 0.005782 | | | 0.50
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 219 ave 219 max 219 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3046 ave 3046 max 3046 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3046
Ave neighs/atom = 7.615
Neighbor list builds = 47
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

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LAMMPS (15 Feb 2016)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.16784 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026
Loop time of 0.513848 on 4 procs for 2000 steps with 400 atoms
Performance: 672572.269 tau/day, 3892.201 timesteps/s
88.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19352 | 0.21426 | 0.23184 | 3.0 | 41.70
Neigh | 0.0034561 | 0.0036583 | 0.0038161 | 0.3 | 0.71
Comm | 0.10711 | 0.12693 | 0.14494 | 4.6 | 24.70
Output | 0.0016916 | 0.0017142 | 0.0017467 | 0.1 | 0.33
Modify | 0.14238 | 0.15759 | 0.16878 | 2.4 | 30.67
Other | | 0.009694 | | | 1.89
Nlocal: 100 ave 113 max 85 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 149.75 ave 160 max 141 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 757.75 ave 885 max 592 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 3031
Ave neighs/atom = 7.5775
Neighbor list builds = 140
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.16867 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026
2100 2.0067383 -3.4164295 -1.402453 0.63163513 1121.7026
2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
2300 2.0418708 -3.4552617 -1.4277716 0.58834191 1121.7026
2400 2.0126625 -3.4242024 -1.3839097 0.80723766 1121.7026
2500 1.9403968 -3.3489494 -1.3995212 0.79492647 1121.7026
2600 2.0459318 -3.4600945 -1.4229599 0.69698729 1121.7026
2700 2.0032338 -3.4126541 -1.4297892 0.44208354 1121.7026
2800 1.9367789 -3.3456765 -1.4171038 0.6873665 1121.7026
2900 1.9870979 -3.3983434 -1.4218523 0.42398659 1121.7026
3000 1.965491 -3.376773 -1.3835208 0.66112051 1121.7026
3100 1.9307633 -3.3342121 -1.3895745 0.45224657 1121.7026
3200 1.8918453 -3.2949278 -1.4157216 0.56825582 1121.7026
3300 1.8824584 -3.2844031 -1.4066487 0.85795659 1121.7026
3400 1.8871451 -3.2878452 -1.4156691 0.91410213 1121.7026
3500 1.9297625 -3.3340904 -1.3901995 0.6754809 1121.7026
3600 1.8994197 -3.3009141 -1.3964162 0.58676937 1121.7026
3700 1.9181765 -3.3204193 -1.3956433 0.54632736 1121.7026
3800 1.9278078 -3.3300748 -1.3999307 0.48904879 1121.7026
3900 1.888321 -3.2896024 -1.3848249 0.49521159 1121.7026
4000 1.8372182 -3.2347372 -1.4091759 0.61895915 1121.7026
Loop time of 0.373834 on 4 procs for 2000 steps with 400 atoms
Performance: 924475.349 tau/day, 5349.973 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25404 | 0.26703 | 0.29737 | 3.4 | 71.43
Neigh | 0.0014787 | 0.0016722 | 0.0018535 | 0.3 | 0.45
Comm | 0.036186 | 0.068545 | 0.082895 | 7.2 | 18.34
Output | 0.00050688 | 0.00052452 | 0.00055194 | 0.1 | 0.14
Modify | 0.025374 | 0.027727 | 0.030269 | 1.1 | 7.42
Other | | 0.008336 | | | 2.23
Nlocal: 100 ave 106 max 92 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 148 ave 152 max 145 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 760.25 ave 815 max 713 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 3041
Ave neighs/atom = 7.6025
Neighbor list builds = 46
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.17878 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
Loop time of 1.79538 on 1 procs for 2000 steps with 400 atoms
Performance: 192494.490 tau/day, 1113.973 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.582 | 1.582 | 1.582 | 0.0 | 88.12
Neigh | 0.013545 | 0.013545 | 0.013545 | 0.0 | 0.75
Comm | 0.0087712 | 0.0087712 | 0.0087712 | 0.0 | 0.49
Output | 0.00034428 | 0.00034428 | 0.00034428 | 0.0 | 0.02
Modify | 0.18736 | 0.18736 | 0.18736 | 0.0 | 10.44
Other | | 0.003359 | | | 0.19
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 216 ave 216 max 216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1929 ave 1929 max 1929 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1929
Ave neighs/atom = 4.8225
Neighbor list builds = 177
Dangerous builds = 146
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.18079 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587
2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587
2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587
3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587
3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587
3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587
3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587
3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587
3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587
3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587
3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587
3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587
4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587
Loop time of 3.05676 on 1 procs for 2000 steps with 400 atoms
Performance: 113061.044 tau/day, 654.288 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9201 | 2.9201 | 2.9201 | 0.0 | 95.53
Neigh | 0.0051684 | 0.0051684 | 0.0051684 | 0.0 | 0.17
Comm | 0.011668 | 0.011668 | 0.011668 | 0.0 | 0.38
Output | 0.00038481 | 0.00038481 | 0.00038481 | 0.0 | 0.01
Modify | 0.1134 | 0.1134 | 0.1134 | 0.0 | 3.71
Other | | 0.00608 | | | 0.20
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 204 ave 204 max 204 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1857 ave 1857 max 1857 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1857
Ave neighs/atom = 4.6425
Neighbor list builds = 48
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (15 Feb 2016)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.16784 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
Loop time of 0.543654 on 4 procs for 2000 steps with 400 atoms
Performance: 635698.342 tau/day, 3678.810 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38532 | 0.40127 | 0.41984 | 2.3 | 73.81
Neigh | 0.0035267 | 0.0035982 | 0.0036683 | 0.1 | 0.66
Comm | 0.039163 | 0.057053 | 0.072538 | 5.9 | 10.49
Output | 0.00048089 | 0.00050312 | 0.00056362 | 0.2 | 0.09
Modify | 0.076422 | 0.077282 | 0.078008 | 0.2 | 14.22
Other | | 0.003945 | | | 0.73
Nlocal: 100 ave 108 max 95 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 125.75 ave 128 max 123 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 482.25 ave 535 max 442 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 1929
Ave neighs/atom = 4.8225
Neighbor list builds = 177
Dangerous builds = 146
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.16867 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
2700 1.9608664 0.18459944 2.1483889 1.3461096 1654.9587
2800 2.005755 0.13729992 2.1214078 1.1596183 1654.9587
2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
3000 1.9606373 0.18480426 2.1301691 1.3280548 1654.9587
3100 1.9824235 0.16187647 2.1284433 1.2590074 1654.9587
3200 1.9389485 0.20774113 2.1063219 1.4587339 1654.9587
3300 1.984931 0.15929453 2.1301897 1.2415169 1654.9587
3400 1.9596864 0.18578934 2.1215072 1.3738204 1654.9587
3500 1.9671165 0.17804604 2.0934256 1.3147236 1654.9587
3600 1.9702644 0.17471548 2.156925 1.3331072 1654.9587
3700 1.9104013 0.2379238 2.1305421 1.5831938 1654.9587
3800 1.9129623 0.23512612 2.1445951 1.565741 1654.9587
3900 1.9868116 0.15724371 2.1658058 1.2581725 1654.9587
4000 2.0058633 0.13728433 2.1534403 1.1352037 1654.9587
Loop time of 0.868601 on 4 procs for 2000 steps with 400 atoms
Performance: 397881.371 tau/day, 2302.554 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71894 | 0.74023 | 0.79323 | 3.6 | 85.22
Neigh | 0.0012772 | 0.0013462 | 0.0014431 | 0.2 | 0.15
Comm | 0.037097 | 0.089266 | 0.10999 | 10.2 | 10.28
Output | 0.00050378 | 0.00052214 | 0.00055289 | 0.1 | 0.06
Modify | 0.027847 | 0.028882 | 0.030547 | 0.6 | 3.33
Other | | 0.008352 | | | 0.96
Nlocal: 100 ave 103 max 96 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 118 ave 122 max 115 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 464.25 ave 489 max 449 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1857
Ave neighs/atom = 4.6425
Neighbor list builds = 48
Dangerous builds = 0
Total wall time: 0:00:01