move/mesh time high - use Vektor/Region as mesh/surface?

Submitted by Phil93 on Thu, 11/25/2021 - 18:30

Hello,

briefly about my problem, i have a cylinder where i fill particles and move this cylinder to mix the particles. I quickly notice that even with small numbers of particles (about 10,000) it takes a long time to simulate. To better see where the most time is spent I ran the script with modify_timing verbose.

Memory usage per processor = 101.801 Mbytes
Step Atoms KinEng CPU
3573539 10072 7.9399243e-07 0
3574000 10072 6.1384116e-07 14.104623
3575000 10072 5.0700542e-07 40.335951
3576000 10072 4.3858865e-07 63.591012
3577000 10072 4.0888562e-07 84.244874
3578000 10072 4.1985968e-07 102.35848
3579000 10072 4.7021907e-07 118.95484
3580000 10072 5.5391356e-07 134.98733
3581000 10072 6.6485328e-07 149.76367
3582000 10072 8.0054958e-07 163.02907
3583000 10072 9.5130844e-07 174.0517
3584000 10072 1.1080549e-06 183.73066
3585000 10072 1.2529899e-06 193.4744
3586000 10072 1.3095823e-06 207.65005
3587000 10072 1.2304952e-06 226.64263
3588000 10072 8.8114309e-07 250.41134
3588539 10072 5.8579165e-07 265.37789
Loop time of 265.378 on 4 procs for 15000 steps with 10002 atoms, finish time Mon Nov 15 13:10:02 2021

Pair time (%) = 47.8998 (18.0496)
Neigh time (%) = 1.07666 (0.405707)
Comm time (%) = 3.50507 (1.32078)
Outpt time (%) = 0.363479 (0.136967)
Modfy time (%) = 211.539 (79.7124)
Modify time [0] (%) = 240.618 (90.67)
Modify time [1] (%) = 162.272 (61.1477)
Modify time [2] (%) = 228.752 (86.1985)
Modify time [3] (%) = 214.514 (80.8334)
Other time (%) = 0.993874 (0.374513)
Fix integrator nve/sphere time (%) = 0.897319 (0.338129)
[0] Fix integrator nve/sphere time 0.398141
[1] Fix integrator nve/sphere time 1.64277
[2] Fix integrator nve/sphere time 0.745386
[3] Fix integrator nve/sphere time 0.802974
Fix gravi gravity time (%) = 0.302223 (0.113884)
[0] Fix gravi gravity time 0.136911
[1] Fix gravi gravity time 0.532499
[2] Fix gravi gravity time 0.235688
[3] Fix gravi gravity time 0.303794
Fix m1 property/global time (%) = 1.71014e-07 (6.44417e-08)
[0] Fix m1 property/global time 1.95112e-07
[1] Fix m1 property/global time 1.97906e-07
[2] Fix m1 property/global time 1.93249e-07
[3] Fix m1 property/global time 9.77889e-08
Fix m2 property/global time (%) = 1.59256e-07 (6.00111e-08)
[0] Fix m2 property/global time 1.14087e-07
[1] Fix m2 property/global time 2.84985e-07
[2] Fix m2 property/global time 1.2666e-07
[3] Fix m2 property/global time 1.11293e-07
Fix m3 property/global time (%) = 1.05589e-07 (3.9788e-08)
[0] Fix m3 property/global time 1.02911e-07
[1] Fix m3 property/global time 1.20141e-07
[2] Fix m3 property/global time 9.49949e-08
[3] Fix m3 property/global time 1.04308e-07
Fix m4 property/global time (%) = 3.00352e-08 (1.13179e-08)
[0] Fix m4 property/global time 2.84053e-08
[1] Fix m4 property/global time 2.79397e-08
[2] Fix m4 property/global time 3.58559e-08
[3] Fix m4 property/global time 2.79397e-08
Fix m5 property/global time (%) = 3.83006e-08 (1.44325e-08)
[0] Fix m5 property/global time 4.23752e-08
[1] Fix m5 property/global time 2.79397e-08
[2] Fix m5 property/global time 3.58559e-08
[3] Fix m5 property/global time 4.70318e-08
Fix m6 property/global time (%) = 5.33182e-08 (2.00914e-08)
[0] Fix m6 property/global time 2.93367e-08
[1] Fix m6 property/global time 1.19675e-07
[2] Fix m6 property/global time 3.63216e-08
[3] Fix m6 property/global time 2.79397e-08
Fix cad1 mesh/surface time (%) = 2.62806 (0.990307)
[0] Fix cad1 mesh/surface time 3.53631
[1] Fix cad1 mesh/surface time 1.62069
[2] Fix cad1 mesh/surface time 2.85243
[3] Fix cad1 mesh/surface time 2.5028
Fix walls wall/gran time (%) = 56.002 (21.1027)
[0] Fix walls wall/gran time 37.9042
[1] Fix walls wall/gran time 74.0822
[2] Fix walls wall/gran time 57.6584
[3] Fix walls wall/gran time 54.3633
Fix wall_neighlist_cad1 neighlist/mesh time (%) = 2.44165 (0.920065)
[0] Fix wall_neighlist_cad1 neighlist/mesh time 2.45988
[1] Fix wall_neighlist_cad1 neighlist/mesh time 2.39902
[2] Fix wall_neighlist_cad1 neighlist/mesh time 2.45066
[3] Fix wall_neighlist_cad1 neighlist/mesh time 2.45703
Fix n_neighs_mesh_cad1 property/atom time (%) = 3.69207e-05 (1.39125e-05)
[0] Fix n_neighs_mesh_cad1 property/atom time 4.26401e-05
[1] Fix n_neighs_mesh_cad1 property/atom time 3.64822e-05
[2] Fix n_neighs_mesh_cad1 property/atom time 3.63854e-05
[3] Fix n_neighs_mesh_cad1 property/atom time 3.21749e-05
Fix tracker_cad1 contacthistory/mesh time (%) = 0.0552855 (0.0208328)
[0] Fix tracker_cad1 contacthistory/mesh time 0.0408954
[1] Fix tracker_cad1 contacthistory/mesh time 0.0697974
[2] Fix tracker_cad1 contacthistory/mesh time 0.064045
[3] Fix tracker_cad1 contacthistory/mesh time 0.0464044
Fix pts1 particletemplate/sphere time (%) = 1.51573e-07 (5.71158e-08)
[0] Fix pts1 particletemplate/sphere time 1.87196e-07
[1] Fix pts1 particletemplate/sphere time 1.1595e-07
[2] Fix pts1 particletemplate/sphere time 1.26194e-07
[3] Fix pts1 particletemplate/sphere time 1.76951e-07
Fix pts2 particletemplate/sphere time (%) = 1.06171e-07 (4.00074e-08)
[0] Fix pts2 particletemplate/sphere time 9.49949e-08
[1] Fix pts2 particletemplate/sphere time 1.16881e-07
[2] Fix pts2 particletemplate/sphere time 1.08965e-07
[3] Fix pts2 particletemplate/sphere time 1.03842e-07
Fix pts3 particletemplate/sphere time (%) = 1.58907e-07 (5.98795e-08)
[0] Fix pts3 particletemplate/sphere time 3.28757e-07
[1] Fix pts3 particletemplate/sphere time 1.08033e-07
[2] Fix pts3 particletemplate/sphere time 1.03842e-07
[3] Fix pts3 particletemplate/sphere time 9.49949e-08
Fix pts4 particletemplate/sphere time (%) = 1.03726e-07 (3.90862e-08)
[0] Fix pts4 particletemplate/sphere time 1.0198e-07
[1] Fix pts4 particletemplate/sphere time 1.00117e-07
[2] Fix pts4 particletemplate/sphere time 1.13156e-07
[3] Fix pts4 particletemplate/sphere time 9.96515e-08
Fix pdd1 particledistribution/discrete time (%) = 2.39466e-07 (9.0236e-08)
[0] Fix pdd1 particledistribution/discrete time 1.7602e-07
[1] Fix pdd1 particledistribution/discrete time 4.17698e-07
[2] Fix pdd1 particledistribution/discrete time 1.7602e-07
[3] Fix pdd1 particledistribution/discrete time 1.88127e-07
Fix pdd2 particledistribution/discrete time (%) = 1.02096e-07 (3.8472e-08)
[0] Fix pdd2 particledistribution/discrete time 9.82545e-08
[1] Fix pdd2 particledistribution/discrete time 1.02911e-07
[2] Fix pdd2 particledistribution/discrete time 1.05239e-07
[3] Fix pdd2 particledistribution/discrete time 1.0198e-07
Fix ins_mesh mesh/surface/planar time (%) = 0.089692 (0.0337978)
[0] Fix ins_mesh mesh/surface/planar time 0.0846828
[1] Fix ins_mesh mesh/surface/planar time 0.127146
[2] Fix ins_mesh mesh/surface/planar time 0.0658182
[3] Fix ins_mesh mesh/surface/planar time 0.081121
Fix ts_check check/timestep/gran time (%) = 1.79163e-07 (6.75125e-08)
[0] Fix ts_check check/timestep/gran time 1.7602e-07
[1] Fix ts_check check/timestep/gran time 1.7602e-07
[2] Fix ts_check check/timestep/gran time 1.85333e-07
[3] Fix ts_check check/timestep/gran time 1.7928e-07
Fix contacthistory contacthistory time (%) = 0.0472053 (0.017788)
[0] Fix contacthistory contacthistory time 0.0244326
[1] Fix contacthistory contacthistory time 0.0837765
[2] Fix contacthistory contacthistory time 0.0401743
[3] Fix contacthistory contacthistory time 0.0404379
Fix cad1 move/mesh time (%) = 139.184 (52.4475)
[0] Fix cad1 move/mesh time 186.884
[1] Fix cad1 move/mesh time 72.0873
[2] Fix cad1 move/mesh time 153.238
[3] Fix cad1 move/mesh time 144.527
Fix cad2 move/mesh time (%) = 9.89149 (3.72732)
[0] Fix cad2 move/mesh time 9.14835
[1] Fix cad2 move/mesh time 9.62718
[2] Fix cad2 move/mesh time 11.4011
[3] Fix cad2 move/mesh time 9.3893

Nlocal: 2518 ave 8400 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 582.5 ave 1446 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 198924 ave 678539 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1

Total # of neighbors = 795694
Ave neighs/atom = 79.0006
Neighbor list builds = 85
Dangerous builds = 0

As you can see above the movement of the mesh Cad1 and Cad2 consumes the most time. So I was wondering if it is possible to define a vector like region command cylinder as mesh/surface and fill the particles there and move this? Does anyone know if this is possible and if so how?

Or does anyone happen to know why the movement takes so much time? Movement Cad1 is linear and Cad2 is rotate.

Thanks for your help

Phil

Phil93 | Thu, 11/25/2021 - 20:10

Thank you for your reply.

Currently there are about 3176 triangles. Unfortunately, I do not know the length.

This is also my plan, if there is no "better" option. Had hoped that maybe like with the region command you can create a cylinder that can be used like an STL.

jumlouh | Tue, 01/23/2024 - 04:19

Nlocal: 2518 ave 8400 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 582.5 ave 1446 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 198924 ave 678539 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
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