Note
Go to the end to download the full example code.
Tracking particles by id in SPH#
This simple example shows how to track particles by id
9 import shamrock
10
11 # Particle tracking is an experimental feature
12 shamrock.enable_experimental_features()
13
14 # If we use the shamrock executable to run this script instead of the python interpreter,
15 # we should not initialize the system as the shamrock executable needs to handle specific MPI logic
16 if not shamrock.sys.is_initialized():
17 shamrock.change_loglevel(1)
18 shamrock.sys.init("0:0")
19
20
21 def is_in_sphere(pt):
22 x, y, z = pt
23 return (x**2 + y**2 + z**2) < 1
Setup parameters
Setup
41 ctx = shamrock.Context()
42 ctx.pdata_layout_new()
43
44 model = shamrock.get_Model_SPH(context=ctx, vector_type="f64_3", sph_kernel="M4")
45
46 cfg = model.gen_default_config()
47 # cfg.set_artif_viscosity_VaryingMM97(alpha_min = 0.1,alpha_max = 1,sigma_decay = 0.1, alpha_u = 1, beta_AV = 2)
48 # cfg.set_artif_viscosity_ConstantDisc(alpha_u=alpha_u, alpha_AV=alpha_AV, beta_AV=beta_AV)
49 # cfg.set_eos_locally_isothermalLP07(cs0=cs0, q=q, r0=r0)
50 cfg.set_artif_viscosity_VaryingCD10(
51 alpha_min=0.0, alpha_max=1, sigma_decay=0.1, alpha_u=1, beta_AV=2
52 )
53 cfg.set_particle_tracking(True)
54 cfg.set_boundary_periodic()
55 cfg.set_eos_adiabatic(1.00001)
56 cfg.print_status()
57 model.set_solver_config(cfg)
58
59 model.init_scheduler(int(1e7), 1)
60
61 bmin = (-bsize, -bsize, -bsize)
62 bmax = (bsize, bsize, bsize)
63 model.resize_simulation_box(bmin, bmax)
64
65 model.set_particle_mass(pmass)
66
67 setup = model.get_setup()
68 lat = setup.make_generator_lattice_hcp(dr, (-bsize, -bsize, -bsize), (bsize, bsize, bsize))
69
70 thesphere = setup.make_modifier_filter(parent=lat, filter=is_in_sphere)
71
72 offset_sphere = setup.make_modifier_offset(
73 parent=thesphere, offset_position=(3.0, 3.0, 3.0), offset_velocity=(-1.0, -1.0, -1.0)
74 )
75
76 setup.apply_setup(offset_sphere)
77
78 model.set_value_in_a_box("uint", "f64", 1, bmin, bmax)
79
80 model.set_cfl_cour(C_cour)
81 model.set_cfl_force(C_force)
82
83 model.change_htolerance(1.3)
84 model.timestep()
85 model.change_htolerance(1.1)
----- SPH Solver configuration -----
[
{
"artif_viscosity": {
"alpha_max": 1.0,
"alpha_min": 0.0,
"alpha_u": 1.0,
"av_type": "varying_cd10",
"beta_AV": 2.0,
"sigma_decay": 0.1
},
"boundary_config": {
"bc_type": "periodic"
},
"cfl_config": {
"cfl_cour": 0.0,
"cfl_force": 0.0,
"cfl_multiplier_stiffness": 2.0,
"eta_sink": 0.05
},
"combined_dtdiv_divcurlv_compute": false,
"debug_dump_filename": "",
"do_debug_dump": false,
"enable_particle_reordering": false,
"eos_config": {
"Tvec": "f64_3",
"eos_type": "adiabatic",
"gamma": 1.00001
},
"epsilon_h": 1e-06,
"ext_force_config": {
"force_list": []
},
"gpart_mass": 0.0,
"h_iter_per_subcycles": 50,
"h_max_subcycles_count": 100,
"htol_up_coarse_cycle": 1.1,
"htol_up_fine_cycle": 1.1,
"kernel_id": "M4<f64>",
"mhd_config": {
"mhd_type": "none"
},
"particle_killing": [],
"particle_reordering_step_freq": 1000,
"show_neigh_stats": false,
"smoothing_length_config": {
"type": "density_based"
},
"time_state": {
"cfl_multiplier": 0.01,
"dt_sph": 0.0,
"time": 0.0
},
"tree_reduction_level": 3,
"type_id": "sycl::vec<f64,3>",
"unit_sys": null,
"use_two_stage_search": true
}
]
------------------------------------
---------------------------- WARNING ----------------------------
Warning: Experimental features are enabled
-----------------------------------------------------------------
Info: pushing data in scheduler, N = 735 [DataInserterUtility][rank=0]
Info: reattributing data ... [DataInserterUtility][rank=0]
Info: reattributing data done in 1690.36 us [DataInserterUtility][rank=0]
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 5.11 us (54.4%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1733.00 ns (0.4%)
patch tree reduce : 651.00 ns (0.1%)
gen split merge : 671.00 ns (0.2%)
split / merge op : 0/0
apply split merge : 1102.00 ns (0.3%)
LB compute : 423.38 us (97.5%)
LB move op cnt : 0
LB apply : 2.93 us (0.7%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.37 us (68.9%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1683.00 ns (0.5%)
patch tree reduce : 330.00 ns (0.1%)
gen split merge : 380.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 271.00 ns (0.1%)
LB compute : 333.35 us (93.6%)
LB move op cnt : 0
LB apply : 16.88 us (4.7%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.27 us (65.6%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1743.00 ns (0.5%)
patch tree reduce : 340.00 ns (0.1%)
gen split merge : 401.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 271.00 ns (0.1%)
LB compute : 353.07 us (97.9%)
LB move op cnt : 0
LB apply : 1853.00 ns (0.5%)
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: Final load balancing step 0 of 3 [SPH setup][rank=0]
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.60 us (60.3%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1392.00 ns (0.4%)
patch tree reduce : 381.00 ns (0.1%)
gen split merge : 370.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 260.00 ns (0.1%)
LB compute : 321.15 us (97.8%)
LB move op cnt : 0
LB apply : 1753.00 ns (0.5%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.60 us (69.0%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1333.00 ns (0.4%)
patch tree reduce : 301.00 ns (0.1%)
gen split merge : 361.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 271.00 ns (0.1%)
LB compute : 331.06 us (97.9%)
LB move op cnt : 0
LB apply : 1814.00 ns (0.5%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.52 us (65.7%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1773.00 ns (0.5%)
patch tree reduce : 331.00 ns (0.1%)
gen split merge : 401.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 281.00 ns (0.1%)
LB compute : 327.72 us (97.8%)
LB move op cnt : 0
LB apply : 1713.00 ns (0.5%)
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: Final load balancing step 1 of 3 [SPH setup][rank=0]
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.44 us (63.4%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1282.00 ns (0.4%)
patch tree reduce : 330.00 ns (0.1%)
gen split merge : 371.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 241.00 ns (0.1%)
LB compute : 335.35 us (98.0%)
LB move op cnt : 0
LB apply : 1753.00 ns (0.5%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.21 us (68.0%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1292.00 ns (0.4%)
patch tree reduce : 290.00 ns (0.1%)
gen split merge : 371.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 230.00 ns (0.1%)
LB compute : 333.09 us (97.9%)
LB move op cnt : 0
LB apply : 1844.00 ns (0.5%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.49 us (69.7%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1323.00 ns (0.4%)
patch tree reduce : 331.00 ns (0.1%)
gen split merge : 380.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 251.00 ns (0.1%)
LB compute : 306.45 us (97.8%)
LB move op cnt : 0
LB apply : 1743.00 ns (0.6%)
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: Final load balancing step 2 of 3 [SPH setup][rank=0]
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.38 us (63.9%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1323.00 ns (0.4%)
patch tree reduce : 331.00 ns (0.1%)
gen split merge : 391.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 290.00 ns (0.1%)
LB compute : 313.66 us (97.8%)
LB move op cnt : 0
LB apply : 1794.00 ns (0.6%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.52 us (70.3%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1282.00 ns (0.4%)
patch tree reduce : 301.00 ns (0.1%)
gen split merge : 391.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 230.00 ns (0.1%)
LB compute : 310.71 us (97.9%)
LB move op cnt : 0
LB apply : 1794.00 ns (0.6%)
Info: Compute load ... [DataInserterUtility][rank=0]
Info: run scheduler step ... [DataInserterUtility][rank=0]
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.29 us (69.2%)
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 1624.00 ns (0.5%)
patch tree reduce : 321.00 ns (0.1%)
gen split merge : 380.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 241.00 ns (0.1%)
LB compute : 293.53 us (97.6%)
LB move op cnt : 0
LB apply : 1724.00 ns (0.6%)
Info: --------------------------------------------- [DataInserterUtility][rank=0]
Info: the setup took : 0.08758681800000001 s [SPH setup][rank=0]
Warning: .change_htolerance(val) is deprecated, [SPH][rank=0]
-> calling this is replaced internally by .change_htolerances(coarse=val, fine=min(val, 1.1))
see: https://shamrock-code.github.io/Shamrock/mkdocs/models/sph/smoothing_length_tolerance
---------------- t = 0, dt = 0 ----------------
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 3.51 us (1.0%)
patch tree reduce : 351.00 ns (0.1%)
gen split merge : 401.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 350.00 ns (0.1%)
LB compute : 349.00 us (97.2%)
LB move op cnt : 0
LB apply : 1983.00 ns (0.6%)
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.42 us (71.2%)
Warning: smoothing length is not converged, rerunning the iterator ... [Smoothinglength][rank=0]
largest h = 0.13 unconverged cnt = 735
Warning: High interface/patch volume ratio. [InterfaceGen][rank=0]
This can lead to high mpi overhead, try to increase the patch split crit
patch 0 high interf/patch volume: 0.20952380952380953
Warning: smoothing length is not converged, rerunning the iterator ... [Smoothinglength][rank=0]
largest h = 0.169 unconverged cnt = 735
Warning: High interface/patch volume ratio. [InterfaceGen][rank=0]
This can lead to high mpi overhead, try to increase the patch split crit
patch 0 high interf/patch volume: 0.39319727891156464
Warning: smoothing length is not converged, rerunning the iterator ... [Smoothinglength][rank=0]
largest h = 0.21970000000000003 unconverged cnt = 334
Warning: High interface/patch volume ratio. [InterfaceGen][rank=0]
This can lead to high mpi overhead, try to increase the patch split crit
patch 0 high interf/patch volume: 0.6585034013605442
Warning: smoothing length is not converged, rerunning the iterator ... [Smoothinglength][rank=0]
largest h = 0.28561000000000003 unconverged cnt = 2
Warning: High interface/patch volume ratio. [InterfaceGen][rank=0]
This can lead to high mpi overhead, try to increase the patch split crit
patch 0 high interf/patch volume: 1.23265306122449
Info: conservation infos : [sph::Model][rank=0]
sum v = (-735,-735,-735)
sum a = (-3.333921680392926e-18,-4.743384504624082e-20,-5.421010862427522e-19)
sum e = 1837.5
sum de = -5.095750210681871e-18
Info: CFL hydro = 0.1305431643141646 sink sink = inf [SPH][rank=0]
Info: cfl dt = 0.1305431643141646 cfl multiplier : 0.01 [sph::Model][rank=0]
Info: processing rate infos : [sph::Model][rank=0]
---------------------------------------------------------------------------------------
| rank | rate (N.s^-1) | Nobj | t compute (s) | MPI | alloc | mem (max) |
---------------------------------------------------------------------------------------
| 0 | 9.5590e+03 | 735 | 7.689e-02 | 0 % | 2 % | 128.66 MB |
---------------------------------------------------------------------------------------
Info: estimated rate : 0 (tsim/hr) [sph::Model][rank=0]
Warning: .change_htolerance(val) is deprecated, [SPH][rank=0]
-> calling this is replaced internally by .change_htolerances(coarse=val, fine=min(val, 1.1))
see: https://shamrock-code.github.io/Shamrock/mkdocs/models/sph/smoothing_length_tolerance
Init history table
90 part_history = []
91
92 data = ctx.collect_data()
93 print(data)
94
95 part_history = [{} for i in range(len(data["xyz"]))]
96 for i in range(len(data["xyz"])):
97 part_history[data["part_id"][i]] = {
98 "x": [data["xyz"][i][0]],
99 "y": [data["xyz"][i][1]],
100 "z": [data["xyz"][i][2]],
101 }
102
103
104 def append_to_history():
105 data = ctx.collect_data()
106
107 for i in range(len(data["xyz"])):
108 part_history[data["part_id"][i]]["x"].append(data["xyz"][i][0])
109 part_history[data["part_id"][i]]["y"].append(data["xyz"][i][1])
110 part_history[data["part_id"][i]]["z"].append(data["xyz"][i][2])
Info: collected : 1 patches [PatchScheduler][rank=0]
adding -> xyz
adding -> vxyz
adding -> axyz
adding -> axyz_ext
adding -> hpart
adding -> part_id
adding -> uint
adding -> duint
adding -> alpha_AV
adding -> divv
adding -> dtdivv
adding -> curlv
adding -> soundspeed
{'xyz': array([[2.3 , 2.48038476, 2.67340137],
[2.4 , 2.30717968, 2.67340137],
[2.3 , 2.3649147 , 2.83670068],
...,
[3.5 , 3.8660254 , 3. ],
[3.5 , 3.75055535, 3.16329932],
[3.5 , 3.51961524, 3.65319726]], shape=(735, 3)), 'vxyz': array([[-1., -1., -1.],
[-1., -1., -1.],
[-1., -1., -1.],
...,
[-1., -1., -1.],
[-1., -1., -1.],
[-1., -1., -1.]], shape=(735, 3)), 'axyz': array([[-6.07564493e-05, -4.19305177e-05, -3.33234503e-05],
[-5.26819605e-05, -7.21000314e-05, -3.19971073e-05],
[-6.54663258e-05, -6.30451355e-05, -9.79795900e-06],
...,
[ 5.02839018e-05, 8.56177477e-05, 6.48509600e-21],
[ 4.24596463e-05, 6.12386886e-05, 1.61018811e-05],
[ 3.96519461e-05, 5.35753755e-05, 6.75477378e-05]],
shape=(735, 3)), 'axyz_ext': array([[0., 0., 0.],
[0., 0., 0.],
[0., 0., 0.],
...,
[0., 0., 0.],
[0., 0., 0.],
[0., 0., 0.]], shape=(735, 3)), 'hpart': array([0.24340982, 0.26266205, 0.25527829, 0.25617457, 0.26581476,
0.24340982, 0.25653232, 0.24634686, 0.26341738, 0.25208943,
0.22243493, 0.23538249, 0.23538249, 0.21573943, 0.2152501 ,
0.2152501 , 0.2164275 , 0.21643851, 0.21403115, 0.26581476,
0.23478299, 0.26206811, 0.2228041 , 0.26133329, 0.24182531,
0.25208943, 0.22852822, 0.2164275 , 0.22669761, 0.21424214,
0.22104652, 0.21461491, 0.25425536, 0.23756227, 0.22276011,
0.26961698, 0.21620613, 0.21666461, 0.21402392, 0.21403115,
0.25262937, 0.22676156, 0.25262937, 0.22676156, 0.21605986,
0.26362011, 0.23688837, 0.2162894 , 0.23467853, 0.21453074,
0.21643851, 0.21509783, 0.21402392, 0.21408423, 0.21403115,
0.21402392, 0.21402392, 0.21402392, 0.21408423, 0.21402392,
0.21402392, 0.21430489, 0.21402392, 0.21402392, 0.21402392,
0.21402392, 0.21402392, 0.21402392, 0.21402392, 0.25527829,
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Run the sim
115 for i in range(5):
116 model.timestep()
117 append_to_history()
---------------- t = 0, dt = 0.1305431643141646 ----------------
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 40.39 us (3.4%)
patch tree reduce : 1914.00 ns (0.2%)
gen split merge : 721.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 932.00 ns (0.1%)
LB compute : 1135.40 us (95.0%)
LB move op cnt : 0
LB apply : 3.84 us (0.3%)
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 3.13 us (69.2%)
Warning: High interface/patch volume ratio. [InterfaceGen][rank=0]
This can lead to high mpi overhead, try to increase the patch split crit
patch 0 high interf/patch volume: 0.6585034013605442
Info: conservation infos : [sph::Model][rank=0]
sum v = (-735.000000000001,-734.9999999999993,-735.0000000000003)
sum a = (-1.3938774180016766e-17,5.692061405548898e-19,2.8324781756183803e-18)
sum e = 1837.5000000169691
sum de = -4.526544070126981e-18
Info: CFL hydro = 4.438475603539535 sink sink = inf [SPH][rank=0]
Info: cfl dt = 4.438475603539535 cfl multiplier : 0.34 [sph::Model][rank=0]
Info: processing rate infos : [sph::Model][rank=0]
---------------------------------------------------------------------------------------
| rank | rate (N.s^-1) | Nobj | t compute (s) | MPI | alloc | mem (max) |
---------------------------------------------------------------------------------------
| 0 | 2.5117e+04 | 735 | 2.926e-02 | 0 % | 2 % | 128.66 MB |
---------------------------------------------------------------------------------------
Info: estimated rate : 16059.991591659416 (tsim/hr) [sph::Model][rank=0]
Info: collected : 1 patches [PatchScheduler][rank=0]
adding -> xyz
adding -> vxyz
adding -> axyz
adding -> axyz_ext
adding -> hpart
adding -> part_id
adding -> uint
adding -> duint
adding -> alpha_AV
adding -> divv
adding -> dtdivv
adding -> curlv
adding -> soundspeed
---------------- t = 0.1305431643141646, dt = 4.438475603539535 ----------------
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 3.17 us (0.9%)
patch tree reduce : 371.00 ns (0.1%)
gen split merge : 461.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 350.00 ns (0.1%)
LB compute : 360.87 us (97.3%)
LB move op cnt : 0
LB apply : 1994.00 ns (0.5%)
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.73 us (69.9%)
Info: conservation infos : [sph::Model][rank=0]
sum v = (-734.9999999999995,-735.0000000000001,-735)
sum a = (3.733721231496956e-18,2.0464316005663896e-18,-4.472333961502706e-19)
sum e = 1837.5000196165292
sum de = -5.421010862427522e-20
Info: CFL hydro = 7.326603651510656 sink sink = inf [SPH][rank=0]
Info: cfl dt = 7.326603651510656 cfl multiplier : 0.56 [sph::Model][rank=0]
Info: processing rate infos : [sph::Model][rank=0]
---------------------------------------------------------------------------------------
| rank | rate (N.s^-1) | Nobj | t compute (s) | MPI | alloc | mem (max) |
---------------------------------------------------------------------------------------
| 0 | 4.1133e+04 | 735 | 1.787e-02 | 0 % | 1 % | 128.66 MB |
---------------------------------------------------------------------------------------
Info: estimated rate : 894217.0430325401 (tsim/hr) [sph::Model][rank=0]
Info: collected : 1 patches [PatchScheduler][rank=0]
adding -> xyz
adding -> vxyz
adding -> axyz
adding -> axyz_ext
adding -> hpart
adding -> part_id
adding -> uint
adding -> duint
adding -> alpha_AV
adding -> divv
adding -> dtdivv
adding -> curlv
adding -> soundspeed
---------------- t = 4.5690187678536995, dt = 7.326603651510656 ----------------
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 3.17 us (0.8%)
patch tree reduce : 360.00 ns (0.1%)
gen split merge : 380.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 361.00 ns (0.1%)
LB compute : 373.44 us (97.4%)
LB move op cnt : 0
LB apply : 2.01 us (0.5%)
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.64 us (69.1%)
Info: conservation infos : [sph::Model][rank=0]
sum v = (-734.9999999999984,-734.9999999999984,-734.9999999999997)
sum a = (2.303929616531697e-18,5.759824041329242e-19,3.5236570605778894e-19)
sum e = 1837.500053070114
sum de = -7.047314121155779e-18
Info: CFL hydro = 7.86752877531102 sink sink = inf [SPH][rank=0]
Info: cfl dt = 7.86752877531102 cfl multiplier : 0.7066666666666667 [sph::Model][rank=0]
Info: processing rate infos : [sph::Model][rank=0]
---------------------------------------------------------------------------------------
| rank | rate (N.s^-1) | Nobj | t compute (s) | MPI | alloc | mem (max) |
---------------------------------------------------------------------------------------
| 0 | 4.1059e+04 | 735 | 1.790e-02 | 0 % | 1 % | 128.66 MB |
---------------------------------------------------------------------------------------
Info: estimated rate : 1473404.8936745862 (tsim/hr) [sph::Model][rank=0]
Info: collected : 1 patches [PatchScheduler][rank=0]
adding -> xyz
adding -> vxyz
adding -> axyz
adding -> axyz_ext
adding -> hpart
adding -> part_id
adding -> uint
adding -> duint
adding -> alpha_AV
adding -> divv
adding -> dtdivv
adding -> curlv
adding -> soundspeed
---------------- t = 11.895622419364354, dt = 7.86752877531102 ----------------
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 3.11 us (0.9%)
patch tree reduce : 370.00 ns (0.1%)
gen split merge : 381.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 351.00 ns (0.1%)
LB compute : 324.72 us (97.2%)
LB move op cnt : 0
LB apply : 1753.00 ns (0.5%)
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.35 us (70.1%)
Info: conservation infos : [sph::Model][rank=0]
sum v = (-735.000000000001,-735.0000000000011,-734.9999999999999)
sum a = (3.1238575094738597e-18,-7.318364664277155e-19,-5.421010862427522e-19)
sum e = 1837.5000585540129
sum de = 7.914675859144182e-18
Info: CFL hydro = 6.975215125196861 sink sink = inf [SPH][rank=0]
Info: cfl dt = 6.975215125196861 cfl multiplier : 0.8044444444444444 [sph::Model][rank=0]
Info: processing rate infos : [sph::Model][rank=0]
---------------------------------------------------------------------------------------
| rank | rate (N.s^-1) | Nobj | t compute (s) | MPI | alloc | mem (max) |
---------------------------------------------------------------------------------------
| 0 | 4.1243e+04 | 735 | 1.782e-02 | 0 % | 1 % | 128.66 MB |
---------------------------------------------------------------------------------------
Info: estimated rate : 1589294.6914687497 (tsim/hr) [sph::Model][rank=0]
Info: collected : 1 patches [PatchScheduler][rank=0]
adding -> xyz
adding -> vxyz
adding -> axyz
adding -> axyz_ext
adding -> hpart
adding -> part_id
adding -> uint
adding -> duint
adding -> alpha_AV
adding -> divv
adding -> dtdivv
adding -> curlv
adding -> soundspeed
---------------- t = 19.763151194675373, dt = 6.975215125196861 ----------------
Info: summary : [LoadBalance][rank=0]
Info: - strategy "psweep" : max = 735 min = 735 [LoadBalance][rank=0]
Info: - strategy "round robin" : max = 735 min = 735 [LoadBalance][rank=0]
Info: Loadbalance stats : [LoadBalance][rank=0]
npatch = 1
min = 735
max = 735
avg = 735
efficiency = 100.00%
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 3.10 us (0.8%)
patch tree reduce : 391.00 ns (0.1%)
gen split merge : 371.00 ns (0.1%)
split / merge op : 0/0
apply split merge : 351.00 ns (0.1%)
LB compute : 368.66 us (97.4%)
LB move op cnt : 0
LB apply : 1934.00 ns (0.5%)
Info: Scheduler step timings : [Scheduler][rank=0]
metadata sync : 2.35 us (70.4%)
Info: conservation infos : [sph::Model][rank=0]
sum v = (-734.9999999999999,-734.9999999999994,-734.9999999999999)
sum a = (-7.779150587583494e-18,2.439454888092385e-19,1.9244588561617704e-18)
sum e = 1837.50004199778
sum de = 4.4181238528784306e-18
Info: CFL hydro = 6.385989483406739 sink sink = inf [SPH][rank=0]
Info: cfl dt = 6.385989483406739 cfl multiplier : 0.8696296296296296 [sph::Model][rank=0]
Info: processing rate infos : [sph::Model][rank=0]
---------------------------------------------------------------------------------------
| rank | rate (N.s^-1) | Nobj | t compute (s) | MPI | alloc | mem (max) |
---------------------------------------------------------------------------------------
| 0 | 4.1279e+04 | 735 | 1.781e-02 | 0 % | 1 % | 128.66 MB |
---------------------------------------------------------------------------------------
Info: estimated rate : 1410261.3907505262 (tsim/hr) [sph::Model][rank=0]
Info: collected : 1 patches [PatchScheduler][rank=0]
adding -> xyz
adding -> vxyz
adding -> axyz
adding -> axyz_ext
adding -> hpart
adding -> part_id
adding -> uint
adding -> duint
adding -> alpha_AV
adding -> divv
adding -> dtdivv
adding -> curlv
adding -> soundspeed
Plot particles history
121 import matplotlib.pyplot as plt
122 import numpy as np
123 from mpl_toolkits.mplot3d import Axes3D
124
125 fig = plt.figure()
126 ax = fig.add_subplot(111, projection="3d")
127
128 for i in range(len(part_history)):
129 ax.plot(part_history[i]["x"], part_history[i]["y"], part_history[i]["z"], ".-", lw=0.2)
130
131 ax.set_xlabel("X")
132 ax.set_ylabel("Y")
133 ax.set_zlabel("Z")
134
135 ax.set_xlim(-4, 4)
136 ax.set_ylim(-4, 4)
137 ax.set_zlim(-4, 4)
138
139
140 fig = plt.figure()
141 ax = fig.add_subplot(111, projection="3d")
142
143 ax.plot(part_history[0]["x"], part_history[0]["y"], part_history[0]["z"], ".-", lw=0.5, label="0")
144 ax.plot(part_history[1]["x"], part_history[1]["y"], part_history[1]["z"], ".-", lw=0.5, label="1")
145 ax.plot(part_history[2]["x"], part_history[2]["y"], part_history[2]["z"], ".-", lw=0.5, label="2")
146
147 ax.set_xlabel("X")
148 ax.set_ylabel("Y")
149 ax.set_zlabel("Z")
150
151 ax.set_xlim(-4, 4)
152 ax.set_ylim(-4, 4)
153 ax.set_zlim(-4, 4)
154
155 ax.legend()
156
157 plt.show()
Total running time of the script: (0 minutes 2.054 seconds)
Estimated memory usage: 110 MB