203 lines
11 KiB
Groff
203 lines
11 KiB
Groff
LAMMPS (9 Nov 2016)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
|
|
units lj
|
|
lattice fcc 0.8442
|
|
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
|
boundary f f f
|
|
|
|
region ball sphere 0.0 0.0 0.0 5.0
|
|
region box block -10 10 -10 10 -10 10
|
|
region half block -10 0 -10 10 -10 10
|
|
|
|
# add molecule ids so we can use chunk/atom
|
|
fix 0 all property/atom mol ghost yes
|
|
|
|
create_box 2 box
|
|
Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
|
1 by 2 by 2 MPI processor grid
|
|
create_atoms 1 region ball
|
|
Created 2123 atoms
|
|
|
|
pair_style lj/cut 4.0
|
|
pair_coeff * * 1.0 1.0
|
|
mass * 1.0
|
|
set group all mol 1
|
|
2123 settings made for mol
|
|
|
|
# label half the sphere with a different type for better visualization
|
|
set region half type 2
|
|
1142 settings made for type
|
|
|
|
# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
|
|
group ball dynamic all region ball
|
|
dynamic group ball defined
|
|
|
|
neigh_modify delay 2 every 1 check yes
|
|
|
|
minimize 0.0 0.0 1000 10000
|
|
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
|
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 = 4.3
|
|
ghost atom cutoff = 4.3
|
|
binsize = 2.15 -> bins = 16 16 16
|
|
Memory usage per processor = 3.77014 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 0 -6.2285099 0 -6.2285099 -0.38871568
|
|
1000 0 -7.3616908 0 -7.3616908 -9.7399049e-16
|
|
Loop time of 8.29581 on 4 procs for 1000 steps with 2123 atoms
|
|
|
|
89.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
Minimization stats:
|
|
Stopping criterion = max iterations
|
|
Energy initial, next-to-last, final =
|
|
-6.22850993032 -7.36169083402 -7.36169083402
|
|
Force two-norm initial, final = 197.762 3.40861e-12
|
|
Force max component initial, final = 7.88704 1.60379e-13
|
|
Final line search alpha, max atom move = 1 1.60379e-13
|
|
Iterations, force evaluations = 1000 1994
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 5.8462 | 6.8198 | 8.0872 | 34.0 | 82.21
|
|
Neigh | 0.021211 | 0.028936 | 0.035891 | 3.8 | 0.35
|
|
Comm | 0.10672 | 1.3842 | 2.3694 | 76.2 | 16.69
|
|
Output | 2.8e-05 | 3.35e-05 | 5e-05 | 0.2 | 0.00
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
Other | | 0.0629 | | | 0.76
|
|
|
|
Nlocal: 530.75 ave 543 max 514 min
|
|
Histogram: 1 0 0 0 0 0 2 0 0 1
|
|
Nghost: 1058.25 ave 1075 max 1046 min
|
|
Histogram: 1 0 0 2 0 0 0 0 0 1
|
|
Neighs: 67699.8 ave 82013 max 55681 min
|
|
Histogram: 1 1 0 0 0 0 1 0 0 1
|
|
|
|
Total # of neighbors = 270799
|
|
Ave neighs/atom = 127.555
|
|
Neighbor list builds = 11
|
|
Dangerous builds = 0
|
|
reset_timestep 0
|
|
|
|
velocity all create 1.2 12351235
|
|
|
|
fix 1 all nve
|
|
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
|
|
|
|
compute 1 all chunk/atom molecule
|
|
compute 2 ball omega/chunk 1
|
|
compute 3 ball inertia/chunk 1
|
|
|
|
# compute rotational kinetic energy: 1/2 * I * omega**2
|
|
variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
|
|
variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
|
|
variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
|
|
|
|
# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
|
|
|
|
thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
|
thermo 500
|
|
|
|
# dump 1 all atom 100 dump.lammpstrj
|
|
|
|
# dump 2 all movie 10 ball.mp4 type mass
|
|
|
|
# equilibration w/o torque added
|
|
run 1000 post no
|
|
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
|
Neighbor list info ...
|
|
1 neighbor list requests
|
|
update every 1 steps, delay 2 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 4.3
|
|
ghost atom cutoff = 4.3
|
|
binsize = 2.15 -> bins = 16 16 16
|
|
Memory usage per processor = 2.77052 Mbytes
|
|
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
|
0 1.7991521 -7.3616908 51125.265 51125.265 51125.265 0.0040198435 -0.0024237256 0.0011306245 0.4130702 0.15016629 0.032677011
|
|
500 0.90968729 -6.4603004 52559.075 52593.598 52370.876 0.0039073429 -0.0023505431 0.0011032256 0.40121833 0.14529121 0.031870471
|
|
1000 0.80269935 -6.3456699 53966.859 54192.03 54298.931 0.0040875347 -0.0023098179 0.00077010445 0.45083753 0.14456425 0.016101285
|
|
Loop time of 2.3842 on 4 procs for 1000 steps with 2123 atoms
|
|
|
|
89.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
# start spinning the ball. rotation around z should increase and Erot_z should grow
|
|
fix 4 ball addtorque 0.0 0.0 200.0
|
|
run 10000 upto post no
|
|
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
|
Memory usage per processor = 2.77052 Mbytes
|
|
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
|
1000 0.80269935 -6.3456699 53966.859 54192.03 54298.931 0.0040875347 -0.0023098179 0.00077010445 0.45083753 0.14456425 0.016101285
|
|
1500 0.68922642 -6.2266953 54966.109 54681.607 54947.256 0.0038798951 -0.0016325797 0.0099837591 0.41371853 0.072871893 2.7384461
|
|
2000 0.64105167 -6.1739656 54782.995 54570.486 54910.316 0.0034645832 -0.0027243304 0.017763588 0.32878936 0.20251043 8.6633395
|
|
2500 0.69929409 -6.2287557 54307.47 53952.925 54538.409 0.0035199565 -0.0022538001 0.028279733 0.33643732 0.13703004 21.808363
|
|
3000 0.77013056 -6.2945597 53916.743 53801.81 53955.863 0.0039732989 -0.0024543292 0.037182149 0.42559463 0.16204384 37.297319
|
|
3500 0.80807105 -6.3246605 53451.163 53387.178 53474.789 0.0043137676 -0.0020556348 0.047270147 0.49732542 0.11279735 59.743821
|
|
4000 0.81007199 -6.3142362 53334.317 53243.089 53685.963 0.0038548696 -0.0031009535 0.055811043 0.3962745 0.25599044 83.612467
|
|
4500 0.7850954 -6.2735818 53738.002 53682.367 53639.471 0.0033046861 -0.0018472801 0.065975851 0.29343502 0.091594032 116.74129
|
|
5000 0.77992741 -6.2508277 53864.644 53804.867 53877.025 0.0038258186 -0.0028703189 0.073848203 0.39420539 0.2216419 146.91071
|
|
5500 0.79428302 -6.2467907 54353.329 53987.578 54234.062 0.0034715133 -0.0030161617 0.082746129 0.32751699 0.24556875 185.66819
|
|
6000 0.82211943 -6.2549436 54273.545 53195.299 54061.645 0.0030929934 -0.0031282112 0.090458895 0.25960687 0.26027676 221.18813
|
|
6500 0.87630771 -6.2870988 54042.229 53505.982 54492.239 0.0026486452 -0.0024783378 0.10046947 0.18956181 0.1643211 275.02546
|
|
7000 0.88614639 -6.2727488 53701.993 52682.206 53948.142 0.0035384498 -0.0035905797 0.11030427 0.33619131 0.33959641 328.19439
|
|
7500 0.92102182 -6.2787281 53410.068 52577.853 53132.511 0.0033084315 -0.0031776605 0.11973875 0.2923058 0.26545312 380.8902
|
|
8000 0.94010525 -6.2697758 53732.562 53384.271 53795.933 0.0046460009 -0.0032755993 0.12803006 0.5799174 0.28639462 440.90328
|
|
8500 0.95359399 -6.252319 53444.305 53558.444 53789.691 0.0037919474 -0.0035729209 0.13616177 0.38423423 0.34185722 498.63117
|
|
9000 0.98631627 -6.25197 53115.01 54017.327 53955.578 0.0045084495 -0.0034368377 0.14488919 0.53981096 0.31902236 566.34143
|
|
9500 1.0328238 -6.2632597 53287.675 53682.978 53769.692 0.0044595175 -0.0025931203 0.15416363 0.5298739 0.1804895 638.95665
|
|
10000 1.0741755 -6.2667785 53103.657 53319.569 53601.523 0.0059237675 -0.0019561182 0.16445664 0.93173079 0.10201096 724.85302
|
|
Loop time of 21.8398 on 4 procs for 9000 steps with 2123 atoms
|
|
|
|
90.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
# continue without adding more torque. rotation continues at fixed speed
|
|
unfix 4
|
|
run 5000
|
|
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
|
Memory usage per processor = 2.77052 Mbytes
|
|
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
|
10000 1.0741755 -6.2667785 53103.657 53319.569 53601.523 0.0059237675 -0.0019561182 0.16445664 0.93173079 0.10201096 724.85302
|
|
10500 1.0588571 -6.2509381 52374.303 52131.544 55020.367 0.0048843769 -0.0018716797 0.15729531 0.62475047 0.091313217 680.65188
|
|
11000 1.0554911 -6.2471863 52803.345 52177.891 55200.756 0.0042073234 -0.0024283269 0.15742315 0.46735107 0.15384055 683.99392
|
|
11500 1.0559499 -6.2469955 54031.351 52919.728 54882.35 0.0046703444 -0.0016225764 0.15994353 0.58926908 0.06966232 701.99832
|
|
12000 1.0311805 -6.2224471 52812.51 52444.13 55356.101 0.0044986993 -0.0019225732 0.15672327 0.53441759 0.096924293 679.83334
|
|
12500 1.0423882 -6.2339087 52000.562 52043.013 55003.272 0.0038688875 -0.0022935053 0.1548654 0.38917977 0.13687746 659.57977
|
|
13000 1.0548857 -6.2465445 52196.499 52869.024 54622.553 0.0036650563 -0.0025542156 0.1590498 0.35056832 0.17245921 690.88895
|
|
13500 1.0443009 -6.2360149 51921.746 53124.078 54750.325 0.0052756473 -0.0011658069 0.15689119 0.72255483 0.036100621 673.83538
|
|
14000 1.0505583 -6.241923 51861.696 52153.234 54321.531 0.0037119391 -0.00045576703 0.15738082 0.35728798 0.0054167284 672.73745
|
|
14500 1.040343 -6.2316147 52035.588 51680.479 54443.305 0.0026177168 -0.0014795729 0.15428968 0.1782854 0.056567797 648.01978
|
|
15000 1.0404962 -6.2322338 52376.795 51327.453 54677.693 0.0025711787 -0.0021695312 0.15403509 0.17313044 0.12079571 648.66363
|
|
Loop time of 11.9695 on 4 procs for 5000 steps with 2123 atoms
|
|
|
|
Performance: 180458.440 tau/day, 417.728 timesteps/s
|
|
89.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 7.0313 | 8.4017 | 9.6932 | 35.5 | 70.19
|
|
Neigh | 0.97886 | 1.3633 | 1.7406 | 26.8 | 11.39
|
|
Comm | 0.34002 | 2.0227 | 3.7911 | 94.9 | 16.90
|
|
Output | 0.001198 | 0.0015522 | 0.002578 | 1.5 | 0.01
|
|
Modify | 0.12841 | 0.131 | 0.13336 | 0.5 | 1.09
|
|
Other | | 0.04924 | | | 0.41
|
|
|
|
Nlocal: 530.75 ave 534 max 529 min
|
|
Histogram: 1 0 2 0 0 0 0 0 0 1
|
|
Nghost: 1038 ave 1048 max 1029 min
|
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
Neighs: 60482.5 ave 72547 max 49124 min
|
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
|
|
Total # of neighbors = 241930
|
|
Ave neighs/atom = 113.957
|
|
Neighbor list builds = 555
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:44
|