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update log files for ellipse and flow examples

This commit is contained in:
Axel Kohlmeyer 2018-11-28 16:16:19 -05:00
parent 4a8f1a7a08
commit 8e07aaf005
12 changed files with 846 additions and 790 deletions
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examples/ellipse/log.27Nov18.ellipse.gayberne.g++.1 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 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
Time spent = 0.000507116 secs
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 ${dof}
compute_modify rot extra/dof 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 ${dof}
compute_modify 1_temp extra/dof 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes
Step c_rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443419 0 1.8381003 0.035765442 20557.278
200 2.2768798 0 2.3992621 0.046544845 20618.928
300 1.8573086 0 1.9571389 0.04239709 18464.842
400 2.1707875 -0.00045989278 2.2870073 0.066725499 13701.839
500 1.9710982 -0.014545321 2.0486111 0.12205188 8490.5214
600 2.0818888 -0.21572832 1.8356955 0.22333255 4697.3035
700 2.1551458 -0.68175426 1.4003368 0.60385996 2541.157
800 1.8879651 -1.6357045 0.21794544 1.0826917 1444.4484
900 2.1993533 -3.0664068 -0.91036919 3.2142529 925.96691
1000 1.4285977 -4.3962037 -2.9651113 3.1830461 744.91324
1100 1.933074 -4.9398703 -3.0147256 1.4694937 715.30906
1200 2.0872875 -4.5711608 -2.4689861 1.4091154 757.68606
1300 1.8950043 -4.1568789 -2.2487345 0.19138859 846.69407
1400 2.1773467 -3.7905723 -1.6164698 0.55639059 930.77026
1500 1.934954 -3.5505876 -1.6187812 0.2572587 1020.2803
1600 2.083004 -3.2707357 -1.1794873 0.68661802 1088.5587
1700 1.9434093 -3.2434441 -1.3043926 0.72465776 1136.9866
1800 1.9731416 -3.2692426 -1.3364608 0.52887378 1162.1022
1900 2.0618126 -3.2264372 -1.162807 0.93455596 1155.8306
2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713
Loop time of 0.950695 on 1 procs for 2000 steps with 400 atoms
Performance: 363523.513 tau/day, 2103.724 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 | 0.72638 | 0.72638 | 0.72638 | 0.0 | 76.40
Neigh | 0.015026 | 0.015026 | 0.015026 | 0.0 | 1.58
Comm | 0.015169 | 0.015169 | 0.015169 | 0.0 | 1.60
Output | 0.0004487 | 0.0004487 | 0.0004487 | 0.0 | 0.05
Modify | 0.18921 | 0.18921 | 0.18921 | 0.0 | 19.90
Other | | 0.004463 | | | 0.47
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 247 ave 247 max 247 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3021 ave 3021 max 3021 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3021
Ave neighs/atom = 7.5525
Neighbor list builds = 137
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Per MPI rank memory allocation (min/avg/max) = 4.763 | 4.763 | 4.763 Mbytes
Step c_rot E_pair TotEng Press Volume
2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713
2100 1.8880098 -3.3875135 -1.4857102 0.21017294 1125.7713
2200 1.9098636 -3.4103342 -1.5286928 0.58806422 1125.7713
2300 1.9069018 -3.4099451 -1.6100279 0.63472569 1125.7713
2400 1.9773111 -3.4856999 -1.5268537 0.68904663 1125.7713
2500 2.0027582 -3.5144592 -1.4900208 0.59925433 1125.7713
2600 1.9616623 -3.4744355 -1.5230915 0.26873349 1125.7713
2700 1.8601168 -3.3625754 -1.4872109 0.68399005 1125.7713
2800 1.8194253 -3.319084 -1.5148077 0.62537226 1125.7713
2900 1.8465082 -3.3451652 -1.5508026 0.60163613 1125.7713
3000 1.8894551 -3.3918005 -1.5180435 0.61243969 1125.7713
3100 1.866554 -3.3662479 -1.5275331 0.54334005 1125.7713
3200 1.8233715 -3.3204693 -1.5180055 0.82717864 1125.7713
3300 1.7945158 -3.2898507 -1.4976351 0.56745564 1125.7713
3400 1.8242025 -3.3242538 -1.5070312 1.0550995 1125.7713
3500 1.860405 -3.3595757 -1.5138968 0.56959347 1125.7713
3600 1.76951 -3.2635375 -1.5302852 0.47091998 1125.7713
3700 1.7874111 -3.2838743 -1.4858244 0.74507678 1125.7713
3800 1.8084002 -3.3081089 -1.5294313 0.63717641 1125.7713
3900 1.9201118 -3.4261733 -1.4874713 0.4111663 1125.7713
4000 1.9130445 -3.4170846 -1.49357 0.35783848 1125.7713
Loop time of 1.05944 on 1 procs for 2000 steps with 400 atoms
Performance: 326208.857 tau/day, 1887.783 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 | 0.91753 | 0.91753 | 0.91753 | 0.0 | 86.60
Neigh | 0.0072479 | 0.0072479 | 0.0072479 | 0.0 | 0.68
Comm | 0.016155 | 0.016155 | 0.016155 | 0.0 | 1.52
Output | 0.00042105 | 0.00042105 | 0.00042105 | 0.0 | 0.04
Modify | 0.11222 | 0.11222 | 0.11222 | 0.0 | 10.59
Other | | 0.005868 | | | 0.55
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 243 ave 243 max 243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3073 ave 3073 max 3073 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3073
Ave neighs/atom = 7.6825
Neighbor list builds = 46
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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examples/ellipse/log.27Nov18.ellipse.gayberne.g++.4 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 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
Time spent = 0.000466347 secs
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 ${dof}
compute_modify rot extra/dof 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 ${dof}
compute_modify 1_temp extra/dof 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 Mbytes
Step c_rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443419 0 1.8381003 0.035765442 20557.278
200 2.2768798 0 2.3992621 0.046544845 20618.928
300 1.8573086 0 1.9571389 0.04239709 18464.842
400 2.1707875 -0.00045989278 2.2870073 0.066725499 13701.839
500 1.9710982 -0.014545321 2.0486111 0.12205188 8490.5214
600 2.0818888 -0.21572832 1.8356955 0.22333255 4697.3035
700 2.1551458 -0.68175426 1.4003368 0.60385996 2541.157
800 1.8879651 -1.6357045 0.21794544 1.0826917 1444.4484
900 2.1993533 -3.0664068 -0.91036919 3.2142529 925.96691
1000 1.4285977 -4.3962037 -2.9651113 3.1830461 744.91324
1100 1.933074 -4.9398703 -3.0147256 1.4694937 715.30906
1200 2.0872875 -4.5711608 -2.4689861 1.4091154 757.68606
1300 1.8950043 -4.1568789 -2.2487345 0.19138859 846.69407
1400 2.1773467 -3.7905723 -1.6164698 0.55639059 930.77026
1500 1.934954 -3.5505876 -1.6187812 0.2572587 1020.2803
1600 2.083004 -3.2707357 -1.1794873 0.68661802 1088.5587
1700 1.9434093 -3.2434441 -1.3043926 0.72465775 1136.9866
1800 1.9731416 -3.2692426 -1.3364608 0.52887379 1162.1022
1900 2.0618126 -3.2264372 -1.162807 0.93455596 1155.8306
2000 1.894614 -3.3964158 -1.4932323 0.69021875 1125.7713
Loop time of 0.349687 on 4 procs for 2000 steps with 400 atoms
Performance: 988313.640 tau/day, 5719.408 timesteps/s
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17051 | 0.19038 | 0.20513 | 3.1 | 54.44
Neigh | 0.0039656 | 0.0043136 | 0.0049045 | 0.6 | 1.23
Comm | 0.054327 | 0.071206 | 0.087044 | 4.9 | 20.36
Output | 0.00043106 | 0.00062788 | 0.0012097 | 0.0 | 0.18
Modify | 0.072846 | 0.077488 | 0.081302 | 1.2 | 22.16
Other | | 0.005673 | | | 1.62
Nlocal: 100 ave 112 max 84 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 146.75 ave 156 max 137 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 755.25 ave 889 max 589 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3021
Ave neighs/atom = 7.5525
Neighbor list builds = 137
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Per MPI rank memory allocation (min/avg/max) = 4.74 | 4.74 | 4.74 Mbytes
Step c_rot E_pair TotEng Press Volume
2000 1.894614 -3.3964158 -1.4932323 0.69021875 1125.7713
2100 1.8880098 -3.3875135 -1.4857102 0.21017294 1125.7713
2200 1.9098636 -3.4103342 -1.5286928 0.58806421 1125.7713
2300 1.9069019 -3.4099452 -1.610028 0.63472573 1125.7713
2400 1.9773106 -3.4856993 -1.5268537 0.68904883 1125.7713
2500 2.0027578 -3.5144588 -1.4900205 0.59925475 1125.7713
2600 1.9616631 -3.4744364 -1.5230915 0.26873516 1125.7713
2700 1.8601136 -3.362572 -1.487211 0.68399725 1125.7713
2800 1.8194391 -3.3190986 -1.5148092 0.62533318 1125.7713
2900 1.846505 -3.3451617 -1.5508267 0.60156074 1125.7713
3000 1.8894747 -3.3918215 -1.5180241 0.61210219 1125.7713
3100 1.866832 -3.3665537 -1.5276291 0.54222093 1125.7713
3200 1.8233362 -3.320323 -1.5177672 0.82891257 1125.7713
3300 1.7946952 -3.2899252 -1.4974666 0.56782835 1125.7713
3400 1.8283468 -3.3286169 -1.5065958 1.0370934 1125.7713
3500 1.8538134 -3.3526037 -1.5116661 0.58945341 1125.7713
3600 1.7851382 -3.2811082 -1.5306837 0.462114 1125.7713
3700 1.7664573 -3.2622701 -1.4774432 0.86540402 1125.7713
3800 1.8574677 -3.3592552 -1.5196884 0.45146881 1125.7713
3900 1.9139087 -3.4196718 -1.5054647 0.79636137 1125.7713
4000 1.9081675 -3.4146407 -1.5285325 0.69377107 1125.7713
Loop time of 0.379139 on 4 procs for 2000 steps with 400 atoms
Performance: 911539.742 tau/day, 5275.114 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20177 | 0.23758 | 0.28816 | 7.4 | 62.66
Neigh | 0.0015984 | 0.001946 | 0.0022459 | 0.6 | 0.51
Comm | 0.046169 | 0.093409 | 0.13456 | 11.9 | 24.64
Output | 0.00048614 | 0.00087821 | 0.0016096 | 0.0 | 0.23
Modify | 0.02563 | 0.029633 | 0.034698 | 2.0 | 7.82
Other | | 0.01569 | | | 4.14
Nlocal: 100 ave 117 max 87 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 152.5 ave 169 max 131 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 771.25 ave 988 max 612 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 3085
Ave neighs/atom = 7.7125
Neighbor list builds = 45
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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examples/ellipse/log.27Nov18.ellipse.resquared.g++.1 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 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
Time spent = 0.000540733 secs
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 ${dof}
compute_modify rot extra/dof 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 ${dof}
compute_modify 1_temp extra/dof 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair resquared, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes
Step c_rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443419 0 1.8381003 0.035765442 20557.278
200 2.2768798 0 2.3992621 0.046544845 20618.928
300 1.8573086 0 1.9571389 0.04239709 18464.842
400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864
500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958
600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892
700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262
800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933
900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139
1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133
1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229
1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187
1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057
1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359
1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976
1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576
1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102
1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953
1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914
2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751
Loop time of 1.62265 on 1 procs for 2000 steps with 400 atoms
Performance: 212984.850 tau/day, 1232.551 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 | 1.4048 | 1.4048 | 1.4048 | 0.0 | 86.57
Neigh | 0.014643 | 0.014643 | 0.014643 | 0.0 | 0.90
Comm | 0.011678 | 0.011678 | 0.011678 | 0.0 | 0.72
Output | 0.00046086 | 0.00046086 | 0.00046086 | 0.0 | 0.03
Modify | 0.18748 | 0.18748 | 0.18748 | 0.0 | 11.55
Other | | 0.003623 | | | 0.22
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 213 ave 213 max 213 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1884 ave 1884 max 1884 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1884
Ave neighs/atom = 4.71
Neighbor list builds = 177
Dangerous builds = 144
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Per MPI rank memory allocation (min/avg/max) = 4.754 | 4.754 | 4.754 Mbytes
Step c_rot E_pair TotEng Press Volume
2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751
2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751
2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751
2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751
2400 1.9752559 0.16967804 2.1177286 1.3037679 1669.0751
2500 1.978203 0.16642164 2.1631435 1.2908362 1669.0751
2600 1.9587508 0.18695272 2.1506896 1.3513902 1669.0751
2700 1.9654455 0.17997217 2.1247901 1.3360491 1669.0751
2800 1.9870267 0.15716583 2.1207709 1.2045103 1669.0751
2900 1.923066 0.22448724 2.1353571 1.4964299 1669.0751
3000 2.0042113 0.13903206 2.1149788 1.2100652 1669.0751
3100 1.9543697 0.19149442 2.0984704 1.3409703 1669.0751
3200 1.9991114 0.14441985 2.1292353 1.175647 1669.0751
3300 1.9629782 0.18246606 2.1463675 1.3162684 1669.0751
3400 1.9403528 0.2063029 2.1687044 1.4952816 1669.0751
3500 1.9887416 0.15531264 2.1485278 1.2530419 1669.0751
3600 1.9732723 0.1717156 2.1755741 1.2958545 1669.0751
3700 2.0072829 0.13576753 2.1212377 1.1421359 1669.0751
3800 1.9581273 0.18762532 2.1743415 1.3711091 1669.0751
3900 1.9761639 0.16862987 2.1429576 1.3036491 1669.0751
4000 1.9615823 0.18390729 2.12447 1.4179639 1669.0751
Loop time of 2.70201 on 1 procs for 2000 steps with 400 atoms
Performance: 127904.684 tau/day, 740.189 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 | 2.563 | 2.563 | 2.563 | 0.0 | 94.85
Neigh | 0.0056589 | 0.0056589 | 0.0056589 | 0.0 | 0.21
Comm | 0.014635 | 0.014635 | 0.014635 | 0.0 | 0.54
Output | 0.00045729 | 0.00045729 | 0.00045729 | 0.0 | 0.02
Modify | 0.11246 | 0.11246 | 0.11246 | 0.0 | 4.16
Other | | 0.00584 | | | 0.22
Nlocal: 400 ave 400 max 400 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: 1872 ave 1872 max 1872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1872
Ave neighs/atom = 4.68
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 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
Time spent = 0.00047946 secs
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 ${dof}
compute_modify rot extra/dof 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 ${dof}
compute_modify 1_temp extra/dof 357
# equilibrate to shrink box around dilute system
run 2000
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair resquared, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 Mbytes
Step c_rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443419 0 1.8381003 0.035765442 20557.278
200 2.2768798 0 2.3992621 0.046544845 20618.928
300 1.8573086 0 1.9571389 0.04239709 18464.842
400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864
500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958
600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892
700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262
800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933
900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139
1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133
1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229
1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187
1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057
1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359
1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976
1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576
1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102
1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953
1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914
2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751
Loop time of 0.513811 on 4 procs for 2000 steps with 400 atoms
Performance: 672620.799 tau/day, 3892.481 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3553 | 0.36778 | 0.37737 | 1.4 | 71.58
Neigh | 0.0039301 | 0.0040173 | 0.004127 | 0.1 | 0.78
Comm | 0.056627 | 0.065564 | 0.076112 | 3.0 | 12.76
Output | 0.00041318 | 0.00061768 | 0.0012202 | 0.0 | 0.12
Modify | 0.070257 | 0.072503 | 0.074547 | 0.6 | 14.11
Other | | 0.003331 | | | 0.65
Nlocal: 100 ave 108 max 96 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 123.5 ave 125 max 122 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 471 ave 518 max 433 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 1884
Ave neighs/atom = 4.71
Neighbor list builds = 177
Dangerous builds = 144
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Per MPI rank memory allocation (min/avg/max) = 4.739 | 4.739 | 4.739 Mbytes
Step c_rot E_pair TotEng Press Volume
2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751
2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751
2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751
2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751
2400 1.9752559 0.16967804 2.1177286 1.303768 1669.0751
2500 1.978203 0.16642165 2.1631435 1.2908362 1669.0751
2600 1.9587508 0.18695271 2.1506896 1.3513902 1669.0751
2700 1.9654455 0.17997218 2.1247901 1.3360492 1669.0751
2800 1.9870267 0.15716584 2.1207709 1.2045104 1669.0751
2900 1.9230662 0.22448703 2.1353571 1.4964289 1669.0751
3000 2.0042113 0.13903204 2.1149787 1.210065 1669.0751
3100 1.9543694 0.19149467 2.0984705 1.3409714 1669.0751
3200 1.9991114 0.14441984 2.1292354 1.1756471 1669.0751
3300 1.9629781 0.18246618 2.1463676 1.3162687 1669.0751
3400 1.940353 0.20630269 2.1687038 1.4952819 1669.0751
3500 1.9887413 0.15531296 2.1485274 1.2530446 1669.0751
3600 1.9732704 0.17171758 2.1755757 1.295861 1669.0751
3700 2.0072863 0.13576402 2.1212392 1.1421254 1669.0751
3800 1.9581337 0.18761851 2.1743384 1.3710796 1669.0751
3900 1.9761519 0.16864273 2.142963 1.3037308 1669.0751
4000 1.9615865 0.18390288 2.1244667 1.4179575 1669.0751
Loop time of 0.846017 on 4 procs for 2000 steps with 400 atoms
Performance: 408502.313 tau/day, 2364.018 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.63647 | 0.67097 | 0.74711 | 5.4 | 79.31
Neigh | 0.0015061 | 0.0015807 | 0.0017054 | 0.2 | 0.19
Comm | 0.058258 | 0.1341 | 0.16808 | 12.1 | 15.85
Output | 0.00045156 | 0.00077933 | 0.0016997 | 0.0 | 0.09
Modify | 0.028721 | 0.029793 | 0.03152 | 0.6 | 3.52
Other | | 0.0088 | | | 1.04
Nlocal: 100 ave 106 max 97 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 114 ave 117 max 111 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 468 ave 528 max 431 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1872
Ave neighs/atom = 4.68
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:01

185
examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1
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LAMMPS (5 Oct 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 c_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 1.01022 on 1 procs for 2000 steps with 400 atoms
Performance: 342102.068 tau/day, 1979.757 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 | 0.80465 | 0.80465 | 0.80465 | 0.0 | 79.65
Neigh | 0.014326 | 0.014326 | 0.014326 | 0.0 | 1.42
Comm | 0.011179 | 0.011179 | 0.011179 | 0.0 | 1.11
Output | 0.00032926 | 0.00032926 | 0.00032926 | 0.0 | 0.03
Modify | 0.17561 | 0.17561 | 0.17561 | 0.0 | 17.38
Other | | 0.004126 | | | 0.41
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 c_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 1.13656 on 1 procs for 2000 steps with 400 atoms
Performance: 304074.636 tau/day, 1759.691 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 | 1.0076 | 1.0076 | 1.0076 | 0.0 | 88.65
Neigh | 0.0065663 | 0.0065663 | 0.0065663 | 0.0 | 0.58
Comm | 0.011639 | 0.011639 | 0.011639 | 0.0 | 1.02
Output | 0.00035858 | 0.00035858 | 0.00035858 | 0.0 | 0.03
Modify | 0.10463 | 0.10463 | 0.10463 | 0.0 | 9.21
Other | | 0.00581 | | | 0.51
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

185
examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4
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LAMMPS (5 Oct 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 c_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 0.348825 on 4 procs for 2000 steps with 400 atoms
Performance: 990754.062 tau/day, 5733.530 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.18317 | 0.20567 | 0.22597 | 3.3 | 58.96
Neigh | 0.0036285 | 0.0038322 | 0.0039773 | 0.2 | 1.10
Comm | 0.043543 | 0.06339 | 0.085499 | 5.9 | 18.17
Output | 0.00044894 | 0.00046825 | 0.00051665 | 0.1 | 0.13
Modify | 0.069605 | 0.070677 | 0.071795 | 0.3 | 20.26
Other | | 0.004791 | | | 1.37
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 c_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 0.380732 on 4 procs for 2000 steps with 400 atoms
Performance: 907726.114 tau/day, 5253.045 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24119 | 0.25802 | 0.28318 | 3.0 | 67.77
Neigh | 0.001538 | 0.0017161 | 0.0018811 | 0.3 | 0.45
Comm | 0.055332 | 0.081399 | 0.098741 | 5.6 | 21.38
Output | 0.0005157 | 0.00053984 | 0.00058794 | 0.1 | 0.14
Modify | 0.026189 | 0.027282 | 0.029091 | 0.7 | 7.17
Other | | 0.01177 | | | 3.09
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

182
examples/ellipse/log.5Oct16.ellipse.resquared.g++.1
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@ -1,182 +0,0 @@
LAMMPS (5 Oct 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 c_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 1.69003 on 1 procs for 2000 steps with 400 atoms
Performance: 204492.823 tau/day, 1183.408 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 | 1.4827 | 1.4827 | 1.4827 | 0.0 | 87.73
Neigh | 0.014216 | 0.014216 | 0.014216 | 0.0 | 0.84
Comm | 0.0084538 | 0.0084538 | 0.0084538 | 0.0 | 0.50
Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02
Modify | 0.18062 | 0.18062 | 0.18062 | 0.0 | 10.69
Other | | 0.003745 | | | 0.22
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 c_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 2.86686 on 1 procs for 2000 steps with 400 atoms
Performance: 120550.133 tau/day, 697.628 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 | 2.7349 | 2.7349 | 2.7349 | 0.0 | 95.40
Neigh | 0.0052247 | 0.0052247 | 0.0052247 | 0.0 | 0.18
Comm | 0.011207 | 0.011207 | 0.011207 | 0.0 | 0.39
Output | 0.00036931 | 0.00036931 | 0.00036931 | 0.0 | 0.01
Modify | 0.10925 | 0.10925 | 0.10925 | 0.0 | 3.81
Other | | 0.005949 | | | 0.21
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

182
examples/ellipse/log.5Oct16.ellipse.resquared.g++.4
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@ -1,182 +0,0 @@
LAMMPS (5 Oct 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 c_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 0.529177 on 4 procs for 2000 steps with 400 atoms
Performance: 653089.670 tau/day, 3779.454 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 | 0.36797 | 0.3809 | 0.38796 | 1.2 | 71.98
Neigh | 0.0037003 | 0.0038002 | 0.0038807 | 0.1 | 0.72
Comm | 0.057266 | 0.063631 | 0.076821 | 3.1 | 12.02
Output | 0.00050998 | 0.00052881 | 0.00056648 | 0.1 | 0.10
Modify | 0.075577 | 0.076514 | 0.078309 | 0.4 | 14.46
Other | | 0.0038 | | | 0.72
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 c_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 0.822603 on 4 procs for 2000 steps with 400 atoms
Performance: 420129.522 tau/day, 2431.305 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 | 0.67029 | 0.69125 | 0.73659 | 3.2 | 84.03
Neigh | 0.0013115 | 0.0014372 | 0.0016122 | 0.3 | 0.17
Comm | 0.046684 | 0.092118 | 0.1133 | 9.0 | 11.20
Output | 0.00053906 | 0.00055629 | 0.00059342 | 0.1 | 0.07
Modify | 0.026623 | 0.027991 | 0.029785 | 0.8 | 3.40
Other | | 0.009251 | | | 1.12
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

35
examples/flow/log.5Oct16.flow.couette.g++.1 → examples/flow/log.27Nov18.flow.couette.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2-d LJ flow simulation
dimension 2
@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
Time spent = 0.000395536 secs
mass 1 1.0
mass 2 1.0
@ -75,7 +77,7 @@ fix 4 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 500 dump.flow
@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
run 10000
Neighbor list info ...
1 neighbor list requests
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 = 37 32 1
Memory usage per processor = 2.47395 Mbytes
binsize = 0.71123, bins = 37 32 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0644427 -0.31382888 0 0.44395296 3.0013076 571.54286
@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.402333 0 0.30957177 2.4852035 571.54286
9500 0.99889786 -0.46870263 0 0.24241751 2.3763314 571.54286
10000 1 -0.43338695 0 0.27851782 2.405424 571.54286
Loop time of 0.281614 on 1 procs for 10000 steps with 420 atoms
Loop time of 0.293461 on 1 procs for 10000 steps with 420 atoms
Performance: 9204085.735 tau/day, 35509.590 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 8832531.296 tau/day, 34076.124 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 | 0.12437 | 0.12437 | 0.12437 | 0.0 | 44.16
Neigh | 0.062146 | 0.062146 | 0.062146 | 0.0 | 22.07
Comm | 0.0076008 | 0.0076008 | 0.0076008 | 0.0 | 2.70
Output | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 0.05
Modify | 0.067444 | 0.067444 | 0.067444 | 0.0 | 23.95
Other | | 0.01991 | | | 7.07
Pair | 0.11085 | 0.11085 | 0.11085 | 0.0 | 37.77
Neigh | 0.059952 | 0.059952 | 0.059952 | 0.0 | 20.43
Comm | 0.010563 | 0.010563 | 0.010563 | 0.0 | 3.60
Output | 0.00021076 | 0.00021076 | 0.00021076 | 0.0 | 0.07
Modify | 0.089026 | 0.089026 | 0.089026 | 0.0 | 30.34
Other | | 0.02286 | | | 7.79
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

35
examples/flow/log.5Oct16.flow.couette.g++.4 → examples/flow/log.27Nov18.flow.couette.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2-d LJ flow simulation
dimension 2
@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
Time spent = 0.00031352 secs
mass 1 1.0
mass 2 1.0
@ -75,7 +77,7 @@ fix 4 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 500 dump.flow
@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
run 10000
Neighbor list info ...
1 neighbor list requests
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 = 37 32 1
Memory usage per processor = 2.47768 Mbytes
binsize = 0.71123, bins = 37 32 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.048 | 3.048 | 3.048 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0951876 -0.33403931 0 0.44562996 3.2502319 571.54286
@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.45171969 0 0.26018507 2.5525861 571.54286
9500 1.0322994 -0.40989898 0 0.32499991 2.6021234 571.54286
10000 1 -0.42489516 0 0.28700961 2.619505 571.54286
Loop time of 0.134939 on 4 procs for 10000 steps with 420 atoms
Loop time of 0.172876 on 4 procs for 10000 steps with 420 atoms
Performance: 19208643.416 tau/day, 74107.421 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 14993379.796 tau/day, 57844.829 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.024453 | 0.030829 | 0.036954 | 3.5 | 22.85
Neigh | 0.0152 | 0.016832 | 0.018415 | 1.2 | 12.47
Comm | 0.040894 | 0.049385 | 0.058308 | 3.7 | 36.60
Output | 0.00027037 | 0.00029039 | 0.0003438 | 0.2 | 0.22
Modify | 0.017885 | 0.018734 | 0.019774 | 0.6 | 13.88
Other | | 0.01887 | | | 13.98
Pair | 0.024842 | 0.030136 | 0.036735 | 3.1 | 17.43
Neigh | 0.014276 | 0.015892 | 0.017287 | 1.1 | 9.19
Comm | 0.065952 | 0.075937 | 0.084912 | 3.2 | 43.93
Output | 0.00034285 | 0.00042874 | 0.00067973 | 0.0 | 0.25
Modify | 0.024682 | 0.026202 | 0.028216 | 1.0 | 15.16
Other | | 0.02428 | | | 14.05
Nlocal: 105 ave 113 max 97 min
Histogram: 2 0 0 0 0 0 0 0 0 2

35
examples/flow/log.5Oct16.flow.pois.g++.1 → examples/flow/log.27Nov18.flow.pois.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2-d LJ flow simulation
dimension 2
@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
Time spent = 0.000394583 secs
mass 1 1.0
mass 2 1.0
@ -75,7 +77,7 @@ fix 7 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 500 dump.flow
@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
run 10000
Neighbor list info ...
1 neighbor list requests
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 = 37 32 1
Memory usage per processor = 2.47395 Mbytes
binsize = 0.71123, bins = 37 32 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0990751 -0.36396768 0 0.41846911 2.522517 575.55806
@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.74461165 0 -0.032706889 2.574656 498.14523
9500 1.2047533 -0.75768848 0 0.09998113 2.4174997 501.8877
10000 1 -0.67361996 0 0.038284798 2.2310948 507.57444
Loop time of 0.313724 on 1 procs for 10000 steps with 420 atoms
Loop time of 0.353337 on 1 procs for 10000 steps with 420 atoms
Performance: 8262038.165 tau/day, 31875.147 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 7335771.903 tau/day, 28301.589 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13662 | 0.13662 | 0.13662 | 0.0 | 43.55
Neigh | 0.034956 | 0.034956 | 0.034956 | 0.0 | 11.14
Comm | 0.0064242 | 0.0064242 | 0.0064242 | 0.0 | 2.05
Output | 0.00014639 | 0.00014639 | 0.00014639 | 0.0 | 0.05
Modify | 0.11616 | 0.11616 | 0.11616 | 0.0 | 37.03
Other | | 0.01941 | | | 6.19
Pair | 0.12053 | 0.12053 | 0.12053 | 0.0 | 34.11
Neigh | 0.033673 | 0.033673 | 0.033673 | 0.0 | 9.53
Comm | 0.00895 | 0.00895 | 0.00895 | 0.0 | 2.53
Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.07
Modify | 0.16577 | 0.16577 | 0.16577 | 0.0 | 46.92
Other | | 0.02418 | | | 6.84
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

35
examples/flow/log.5Oct16.flow.pois.g++.4 → examples/flow/log.27Nov18.flow.pois.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2-d LJ flow simulation
dimension 2
@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
Time spent = 0.00031805 secs
mass 1 1.0
mass 2 1.0
@ -75,7 +77,7 @@ fix 7 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 500 dump.flow
@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
run 10000
Neighbor list info ...
1 neighbor list requests
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 = 37 32 1
Memory usage per processor = 2.47768 Mbytes
binsize = 0.71123, bins = 37 32 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.048 | 3.048 | 3.048 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0758737 -0.36090417 0 0.40501541 2.7822308 575.0659
@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.8200207 0 -0.10811593 2.6210027 502.60511
9500 1.2167146 -0.77385956 0 0.092325373 2.5938179 500.86068
10000 1 -0.73082779 0 -0.018923029 2.735112 505.69856
Loop time of 0.225282 on 4 procs for 10000 steps with 420 atoms
Loop time of 0.208663 on 4 procs for 10000 steps with 420 atoms
Performance: 11505578.988 tau/day, 44388.808 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 12421919.467 tau/day, 47924.072 timesteps/s
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.032012 | 0.033154 | 0.035252 | 0.7 | 14.72
Neigh | 0.0094411 | 0.0097138 | 0.010069 | 0.2 | 4.31
Comm | 0.080785 | 0.085431 | 0.088782 | 1.0 | 37.92
Output | 0.0003736 | 0.00039834 | 0.00046349 | 0.2 | 0.18
Modify | 0.062812 | 0.064686 | 0.066481 | 0.6 | 28.71
Other | | 0.0319 | | | 14.16
Pair | 0.031368 | 0.032216 | 0.033688 | 0.5 | 15.44
Neigh | 0.0093348 | 0.0097306 | 0.010144 | 0.3 | 4.66
Comm | 0.059824 | 0.065823 | 0.07057 | 1.8 | 31.55
Output | 0.00033283 | 0.00043827 | 0.00073981 | 0.0 | 0.21
Modify | 0.067317 | 0.071492 | 0.075636 | 1.3 | 34.26
Other | | 0.02896 | | | 13.88
Nlocal: 105 ave 106 max 103 min
Histogram: 1 0 0 0 0 0 1 0 0 2