Merge remote-tracking branch 'github/develop' into collected-small-fixes
This commit is contained in:
Axel Kohlmeyer
75
examples/rheo/balloon/in.rheo.balloon
Normal file
75
examples/rheo/balloon/in.rheo.balloon
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@ -0,0 +1,75 @@
|
||||
# ------ 2D water balloon ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -40 40 0 80 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
|
||||
region fluid sphere -10 40 0 30 units box side in
|
||||
lattice hex 1.0
|
||||
create_atoms 1 region fluid
|
||||
|
||||
region shell sphere -10 40 0 27 units box side out
|
||||
group shell region shell
|
||||
|
||||
set group shell rheo/status 1
|
||||
set group all vx 0.005 vy -0.04
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
create_bonds many shell shell 1 0 1.5
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# A lower critical strain allows the balloon to pop
|
||||
#bond_coeff 1 1.0 0.05 1.0
|
||||
|
||||
# ------ Drop balloon ------#
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||
run 30000
|
||||
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
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@ -0,0 +1,382 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D water balloon ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -40 40 0 80 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
Created orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region fluid sphere -10 40 0 30 units box side in
|
||||
lattice hex 1.0
|
||||
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||
create_atoms 1 region fluid
|
||||
Created 2830 atoms
|
||||
using lattice units in orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
region shell sphere -10 40 0 27 units box side out
|
||||
group shell region shell
|
||||
544 atoms in group shell
|
||||
|
||||
set group shell rheo/status 1
|
||||
Setting atom values ...
|
||||
544 settings made for rheo/status
|
||||
set group all vx 0.005 vy -0.04
|
||||
Setting atom values ...
|
||||
2830 settings made for vx
|
||||
2830 settings made for vy
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable kappa equal 0.01*1/${mp}
|
||||
variable kappa equal 0.01*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
create_bonds many shell shell 1 0 1.5
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 49 49 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair rheo, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) pair rheo/solid, perpetual, trim from (2)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Added 1263 bonds, new total = 1263
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
6 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# A lower critical strain allows the balloon to pop
|
||||
#bond_coeff 1 1.0 0.05 1.0
|
||||
|
||||
# ------ Drop balloon ------#
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||
run 30000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 49 49 1
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (1)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.63 | 17.64 | 17.65 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0.0008125 0.00035927734 2830
|
||||
200 20 0.0008125 0.00035927734 2830
|
||||
400 40 0.0008125 0.00035927734 2830
|
||||
600 60 0.0008125 0.00035927734 2830
|
||||
800 80 0.0008125 0.00035927734 2830
|
||||
1000 100 0.0008125 0.00035927734 2830
|
||||
1200 120 0.0008125 0.00035927734 2830
|
||||
1400 140 0.0008125 0.00035927734 2830
|
||||
1600 160 0.0008125 0.00035927734 2830
|
||||
1800 180 0.0008125 0.00035927734 2830
|
||||
2000 200 0.0008125 0.00035927734 2830
|
||||
2200 220 0.0008125 0.00035927734 2830
|
||||
2400 240 0.00079033569 0.00043037861 2830
|
||||
2600 260 0.0007549229 0.00045188383 2830
|
||||
2800 280 0.00072808836 0.00031695003 2830
|
||||
3000 300 0.0007017958 1.6121754e-05 2830
|
||||
3200 320 0.00067479047 -0.00015725514 2830
|
||||
3400 340 0.00064762254 -0.00023361314 2830
|
||||
3600 360 0.00061960255 -0.00033837679 2830
|
||||
3800 380 0.0005857206 -0.00051770716 2830
|
||||
4000 400 0.00055061733 -0.00070309251 2830
|
||||
4200 420 0.00051884719 -0.0008247795 2830
|
||||
4400 440 0.00049022236 -0.00099918413 2830
|
||||
4600 460 0.00046060011 -0.0010923159 2830
|
||||
4800 480 0.00042900173 -0.0011524571 2830
|
||||
5000 500 0.00039751503 -0.0012586358 2830
|
||||
5200 520 0.00036620054 -0.0013973543 2830
|
||||
5400 540 0.00033130023 -0.0015185231 2830
|
||||
5600 560 0.00030565892 -0.0016159836 2830
|
||||
5800 580 0.00028209836 -0.0016925198 2830
|
||||
6000 600 0.00024695044 -0.0017796892 2830
|
||||
6200 620 0.00021190635 -0.0018706272 2830
|
||||
6400 640 0.0001947093 -0.0019146643 2830
|
||||
6600 660 0.00018903936 -0.0019146199 2830
|
||||
6800 680 0.00017753371 -0.0019390155 2830
|
||||
7000 700 0.00015170593 -0.0020247472 2830
|
||||
7200 720 0.00011509692 -0.0021222209 2830
|
||||
7400 740 7.9861785e-05 -0.0022033181 2830
|
||||
7600 760 6.1350463e-05 -0.0022511971 2830
|
||||
7800 780 6.5269523e-05 -0.0022222806 2830
|
||||
8000 800 8.5709569e-05 -0.0021089664 2830
|
||||
8200 820 0.00011746348 -0.0019351493 2830
|
||||
8400 840 0.00015698134 -0.0017079928 2830
|
||||
8600 860 0.00019758065 -0.0014618965 2830
|
||||
8800 880 0.00023338199 -0.0012365832 2830
|
||||
9000 900 0.00026282353 -0.0010348527 2830
|
||||
9200 920 0.00028604776 -0.00085287884 2830
|
||||
9400 940 0.00030388767 -0.000681122 2830
|
||||
9600 960 0.000317589 -0.00052203521 2830
|
||||
9800 980 0.00032716728 -0.00037501187 2830
|
||||
10000 1000 0.00033270692 -0.00025576132 2830
|
||||
10200 1020 0.00033485986 -0.00016554207 2830
|
||||
10400 1040 0.00033476763 -9.8525417e-05 2830
|
||||
10600 1060 0.00033351922 -5.1166347e-05 2830
|
||||
10800 1080 0.00033161645 -2.0773965e-05 2830
|
||||
11000 1100 0.00032913022 2.2384421e-07 2830
|
||||
11200 1120 0.00032618376 1.2304773e-05 2830
|
||||
11400 1140 0.00032310409 1.3725982e-05 2830
|
||||
11600 1160 0.0003202128 9.0431945e-06 2830
|
||||
11800 1180 0.00031760386 -5.3537879e-07 2830
|
||||
12000 1200 0.00031518884 -1.331708e-05 2830
|
||||
12200 1220 0.00031283958 -3.0838612e-05 2830
|
||||
12400 1240 0.0003104901 -5.0038548e-05 2830
|
||||
12600 1260 0.00030811597 -6.9699925e-05 2830
|
||||
12800 1280 0.00030555782 -8.9972287e-05 2830
|
||||
13000 1300 0.00030256671 -0.00011712941 2830
|
||||
13200 1320 0.00029907961 -0.00015495826 2830
|
||||
13400 1340 0.00029504656 -0.00020292633 2830
|
||||
13600 1360 0.0002905184 -0.00024892421 2830
|
||||
13800 1380 0.00028564542 -0.000295085 2830
|
||||
14000 1400 0.00028073246 -0.00034571956 2830
|
||||
14200 1420 0.00027611457 -0.00039341977 2830
|
||||
14400 1440 0.00027217382 -0.0004281012 2830
|
||||
14600 1460 0.00026919129 -0.00045342545 2830
|
||||
14800 1480 0.00026727674 -0.00047323419 2830
|
||||
15000 1500 0.0002663482 -0.00048423944 2830
|
||||
15200 1520 0.00026616663 -0.0004816085 2830
|
||||
15400 1540 0.00026634862 -0.00047573486 2830
|
||||
15600 1560 0.0002664314 -0.00046803192 2830
|
||||
15800 1580 0.00026603348 -0.00045753668 2830
|
||||
16000 1600 0.00026511015 -0.00044676105 2830
|
||||
16200 1620 0.00026373403 -0.00044075794 2830
|
||||
16400 1640 0.00026217342 -0.00043684036 2830
|
||||
16600 1660 0.0002607038 -0.00042774771 2830
|
||||
16800 1680 0.00025951097 -0.00041603026 2830
|
||||
17000 1700 0.00025869088 -0.00040302996 2830
|
||||
17200 1720 0.00025825588 -0.00038415247 2830
|
||||
17400 1740 0.00025818373 -0.00035742127 2830
|
||||
17600 1760 0.00025843381 -0.00032854722 2830
|
||||
17800 1780 0.00025897836 -0.00029821183 2830
|
||||
18000 1800 0.00025981472 -0.00026108907 2830
|
||||
18200 1820 0.00026095775 -0.00021731058 2830
|
||||
18400 1840 0.00026239688 -0.00017030825 2830
|
||||
18600 1860 0.00026404432 -0.00011868778 2830
|
||||
18800 1880 0.00026574247 -5.9556286e-05 2830
|
||||
19000 1900 0.00026729563 2.3014881e-06 2830
|
||||
19200 1920 0.00026852418 6.2100169e-05 2830
|
||||
19400 1940 0.00026929086 0.00012090325 2830
|
||||
19600 1960 0.0002695407 0.00017904223 2830
|
||||
19800 1980 0.00026929677 0.00023112254 2830
|
||||
20000 2000 0.00026863577 0.0002756697 2830
|
||||
20200 2020 0.00026765699 0.0003158399 2830
|
||||
20400 2040 0.00026646841 0.00035200747 2830
|
||||
20600 2060 0.00026516938 0.00038018442 2830
|
||||
20800 2080 0.00026383495 0.00040179111 2830
|
||||
21000 2100 0.00026252489 0.00042030921 2830
|
||||
21200 2120 0.00026128616 0.00043466976 2830
|
||||
21400 2140 0.00026014896 0.00044221445 2830
|
||||
21600 2160 0.00025912325 0.00044531883 2830
|
||||
21800 2180 0.00025821515 0.00044661709 2830
|
||||
22000 2200 0.00025742576 0.00044409089 2830
|
||||
22200 2220 0.00025674938 0.00043634999 2830
|
||||
22400 2240 0.00025617111 0.00042630344 2830
|
||||
22600 2260 0.0002556791 0.00041561603 2830
|
||||
22800 2280 0.00025525963 0.00040166735 2830
|
||||
23000 2300 0.00025489538 0.00038430419 2830
|
||||
23200 2320 0.00025456861 0.0003669402 2830
|
||||
23400 2340 0.00025426747 0.00034972373 2830
|
||||
23600 2360 0.00025398353 0.0003302242 2830
|
||||
23800 2380 0.00025370842 0.00030993088 2830
|
||||
24000 2400 0.00025344084 0.00029143258 2830
|
||||
24200 2420 0.00025318683 0.00027421708 2830
|
||||
24400 2440 0.0002529591 0.00025603123 2830
|
||||
24600 2460 0.0002527713 0.00023950245 2830
|
||||
24800 2480 0.00025264228 0.00022644812 2830
|
||||
25000 2500 0.00025259021 0.00021540748 2830
|
||||
25200 2520 0.00025262892 0.00020544201 2830
|
||||
25400 2540 0.00025276229 0.00019845807 2830
|
||||
25600 2560 0.0002529876 0.00019449958 2830
|
||||
25800 2580 0.00025329374 0.00019082606 2830
|
||||
26000 2600 0.00025366066 0.00018700064 2830
|
||||
26200 2620 0.00025406164 0.00018426061 2830
|
||||
26400 2640 0.00025446737 0.00018098339 2830
|
||||
26600 2660 0.00025484714 0.00017471869 2830
|
||||
26800 2680 0.00025516604 0.00016565557 2830
|
||||
27000 2700 0.00025538911 0.00015493626 2830
|
||||
27200 2720 0.00025548177 0.00014075592 2830
|
||||
27400 2740 0.00025541168 0.00012205573 2830
|
||||
27600 2760 0.00025514889 0.00010039772 2830
|
||||
27800 2780 0.00025467547 7.7069215e-05 2830
|
||||
28000 2800 0.0002539915 5.1158042e-05 2830
|
||||
28200 2820 0.00025312083 2.3468384e-05 2830
|
||||
28400 2840 0.00025211323 -3.2184465e-06 2830
|
||||
28600 2860 0.00025104366 -2.7726301e-05 2830
|
||||
28800 2880 0.00025000263 -5.0202987e-05 2830
|
||||
29000 2900 0.00024907814 -6.9244776e-05 2830
|
||||
29200 2920 0.00024833815 -8.2874516e-05 2830
|
||||
29400 2940 0.0002478155 -9.1854992e-05 2830
|
||||
29600 2960 0.00024750313 -9.766055e-05 2830
|
||||
29800 2980 0.00024735538 -9.9681291e-05 2830
|
||||
30000 3000 0.00024730191 -9.818759e-05 2830
|
||||
Loop time of 177.982 on 4 procs for 30000 steps with 2830 atoms
|
||||
|
||||
Performance: 1456330.235 tau/day, 168.557 timesteps/s, 477.016 katom-step/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 | 22.913 | 27.061 | 34.594 | 87.2 | 15.20
|
||||
Bond | 0.22386 | 0.26159 | 0.30792 | 6.0 | 0.15
|
||||
Neigh | 0.84412 | 0.84509 | 0.8462 | 0.1 | 0.47
|
||||
Comm | 0.50015 | 0.55579 | 0.60346 | 5.2 | 0.31
|
||||
Output | 0.65854 | 0.69412 | 0.72473 | 2.8 | 0.39
|
||||
Modify | 133.13 | 136 | 137.38 | 14.5 | 76.41
|
||||
Other | | 12.57 | | | 7.06
|
||||
|
||||
Nlocal: 707.5 ave 1576 max 53 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 164.75 ave 239 max 94 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 12307.8 ave 27380 max 983 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
FullNghs: 23517 ave 53040 max 1502 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 94068
|
||||
Ave neighs/atom = 33.239576
|
||||
Ave special neighs/atom = 0.89257951
|
||||
Neighbor list builds = 783
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:58
|
||||
76
examples/rheo/dam-break/in.rheo.dam.break
Normal file
76
examples/rheo/dam-break/in.rheo.dam.break
Normal file
@ -0,0 +1,76 @@
|
||||
# ------ 2D dam break ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary f s p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 2.2
|
||||
variable dx equal 3.0
|
||||
|
||||
region box block -1 150 -1 80 -0.1 0.1 units box
|
||||
create_box 2 box
|
||||
lattice hex ${n}
|
||||
|
||||
region fluid block $(xlo+v_dx+1.0) $(xlo+40.0) $(ylo+v_dx+1.0) $(yhi-20.0) EDGE EDGE units box
|
||||
region walls1 block $(xlo+v_dx) $(xhi-v_dx) $(ylo+v_dx) $(yhi-v_dx) EDGE EDGE side out units box
|
||||
region walls2 block EDGE EDGE EDGE $(yhi-v_dx) EDGE EDGE side in units box
|
||||
region walls intersect 2 walls1 walls2
|
||||
|
||||
create_atoms 1 region fluid
|
||||
create_atoms 2 region walls
|
||||
|
||||
group fluid type 1
|
||||
group rig type 2
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable cs equal 1.0
|
||||
variable zeta equal 0.1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.1
|
||||
variable Dr equal 0.1
|
||||
|
||||
mass 1 ${mp}
|
||||
mass 2 $(2*v_mp)
|
||||
set group all rheo/rho ${rho0}
|
||||
|
||||
set group all rheo/status 0
|
||||
set group rig rheo/status 1
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} #rho/damp ${Dr}
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 10 &
|
||||
surface/detection coordination 22 8 &
|
||||
rho/sum
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all gravity 1e-3 vector 0 -1 0
|
||||
fix 5 rig setforce 0.0 0.0 0.0
|
||||
fix 6 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute p all rheo/property/atom pressure
|
||||
compute surf all rheo/property/atom surface
|
||||
compute sn all rheo/property/atom surface/n/x surface/n/y
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time ke press
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho c_surf c_p c_sn[*]
|
||||
|
||||
run 30000
|
||||
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
82
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
82
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
@ -0,0 +1,82 @@
|
||||
# ------ 2D Ice Cube Pour ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
region box block -25 25 0 100 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
|
||||
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
lattice sq 1.0
|
||||
create_atoms 1 region fluid
|
||||
|
||||
set group all sph/e 8.0
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# ------ Pour particles ------#
|
||||
|
||||
molecule my_mol "square.mol"
|
||||
|
||||
# Wall region extends far enough in z to avoid contact
|
||||
region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
|
||||
region drop block -16 16 70 90 EDGE EDGE side in units box
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
thermal &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} &
|
||||
specific/heat * constant ${Cv} &
|
||||
Tfreeze * constant ${Tf} &
|
||||
latent/heat * constant ${L} &
|
||||
react 1.5 1
|
||||
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
|
||||
fix 6 all gravity 5e-4 vector 0 -1 0
|
||||
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
|
||||
fix 8 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||
|
||||
run 30000
|
||||
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
@ -0,0 +1,379 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D Ice Cube Pour ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
region box block -25 25 0 100 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
Created orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 1 $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 1 30 EDGE EDGE units box
|
||||
lattice sq 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
create_atoms 1 region fluid
|
||||
Created 1470 atoms
|
||||
using lattice units in orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
set group all sph/e 8.0
|
||||
Setting atom values ...
|
||||
1470 settings made for sph/e
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable kappa equal 0.01*1/${mp}
|
||||
variable kappa equal 0.01*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# ------ Pour particles ------#
|
||||
|
||||
molecule my_mol "square.mol"
|
||||
Read molecule template my_mol:
|
||||
#Made with create_mol.py
|
||||
1 molecules
|
||||
0 fragments
|
||||
100 atoms with max type 1
|
||||
342 bonds with max type 1
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
|
||||
# Wall region extends far enough in z to avoid contact
|
||||
region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
|
||||
region drop block -16 16 70 90 EDGE EDGE side in units box
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 1 react 1.5 1
|
||||
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
|
||||
fix 6 all gravity 5e-4 vector 0 -1 0
|
||||
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
|
||||
WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1881)
|
||||
fix 8 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||
|
||||
run 30000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
- @article{ApplMathModel.130.310,
|
||||
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||
journal = {Applied Mathematical Modelling},
|
||||
volume = {130},
|
||||
pages = {310-326},
|
||||
year = {2024},
|
||||
issn = {0307-904X},
|
||||
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 31 61 1
|
||||
7 neighbor lists, perpetual/occasional/extra = 6 1 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (4)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) fix rheo/thermal, occasional, trim from (4)
|
||||
attributes: half, newton off, cut 3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.53 | 15.61 | 15.69 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0 0 1470
|
||||
200 20 5.6002982e-05 3.4434234e-05 1570
|
||||
400 40 8.2173099e-05 8.6171768e-05 1570
|
||||
600 60 8.019018e-05 0.00010750355 1570
|
||||
800 80 0.00013866953 0.00010265608 1570
|
||||
1000 100 0.00018965028 8.1985605e-05 1570
|
||||
1200 120 0.00022033242 7.4736443e-05 1670
|
||||
1400 140 0.00030767062 0.00011264333 1670
|
||||
1600 160 0.00040770127 0.00018779992 1670
|
||||
1800 180 0.00047476332 0.00023153009 1670
|
||||
2000 200 0.00059116774 0.00027200445 1670
|
||||
2200 220 0.0007151733 0.0002919963 1770
|
||||
2400 240 0.00083392135 0.00029757889 1770
|
||||
2600 260 0.00099653466 0.00036547269 1770
|
||||
2800 280 0.0011964069 0.00045983458 1770
|
||||
3000 300 0.0013716953 0.00055013647 1770
|
||||
3200 320 0.0015174096 0.00064203572 1870
|
||||
3400 340 0.0016539743 0.00086671622 1870
|
||||
3600 360 0.0015887858 0.00066353749 1870
|
||||
3800 380 0.0016451684 0.00070551483 1870
|
||||
4000 400 0.0017330971 0.00080722283 1870
|
||||
4200 420 0.001812193 0.00073573903 1970
|
||||
4400 440 0.001755871 0.0010621909 1970
|
||||
4600 460 0.0016190772 0.00072913706 1970
|
||||
4800 480 0.0015741931 0.00073524088 1970
|
||||
5000 500 0.0016488815 0.00088684275 1970
|
||||
5200 520 0.0017213288 0.00077042378 2070
|
||||
5400 540 0.0018509598 0.0010219434 2070
|
||||
5600 560 0.0020251064 0.00083182483 2070
|
||||
5800 580 0.0022473255 0.00095076144 2070
|
||||
6000 600 0.0024843519 0.0011247014 2070
|
||||
6200 620 0.0022282321 0.0018105932 2170
|
||||
6400 640 0.0020289063 0.0014158497 2170
|
||||
6600 660 0.002145241 0.0011359383 2170
|
||||
6800 680 0.0024313937 0.0016475504 2170
|
||||
7000 700 0.0021000599 0.0020983745 2170
|
||||
7200 720 0.0019137235 0.0010439152 2270
|
||||
7400 740 0.0018801367 0.00095436448 2270
|
||||
7600 760 0.0017979449 0.0011184039 2270
|
||||
7800 780 0.0018005205 0.0009243205 2270
|
||||
8000 800 0.0017827073 0.0013671228 2270
|
||||
8200 820 0.0018387108 0.0015426012 2270
|
||||
8400 840 0.0016000788 0.0016751514 2270
|
||||
8600 860 0.0013954964 0.0016884335 2270
|
||||
8800 880 0.0013283728 0.0012399398 2270
|
||||
9000 900 0.001389385 0.0012968496 2270
|
||||
9200 920 0.0012295438 0.0012995821 2270
|
||||
9400 940 0.0010522655 0.00082245528 2270
|
||||
9600 960 0.00097085496 0.00053833131 2270
|
||||
9800 980 0.0009398987 0.00063467387 2270
|
||||
10000 1000 0.00092710392 0.00059494446 2270
|
||||
10200 1020 0.00095545471 0.00074560644 2270
|
||||
10400 1040 0.0009645841 0.00085429807 2270
|
||||
10600 1060 0.00064037148 0.0017222246 2270
|
||||
10800 1080 0.00046790978 0.00088204234 2270
|
||||
11000 1100 0.00030106229 0.00074950209 2270
|
||||
11200 1120 0.00027746016 0.00052831745 2270
|
||||
11400 1140 0.0002533348 0.0006272715 2270
|
||||
11600 1160 0.00021825085 0.00029691552 2270
|
||||
11800 1180 0.0001451308 0.00015037478 2270
|
||||
12000 1200 0.0001314823 0.00017227174 2270
|
||||
12200 1220 0.00013693632 0.00017791384 2270
|
||||
12400 1240 0.00014987347 0.0002286677 2270
|
||||
12600 1260 0.00015092598 0.0003698436 2270
|
||||
12800 1280 0.0001291653 0.00047229532 2270
|
||||
13000 1300 0.00011949988 0.00049560375 2270
|
||||
13200 1320 0.00011694665 0.00057542084 2270
|
||||
13400 1340 9.6164519e-05 0.00062714755 2270
|
||||
13600 1360 8.4517591e-05 0.00044156913 2270
|
||||
13800 1380 0.00019140516 0.0003264745 2270
|
||||
14000 1400 0.00013868599 0.00037753497 2270
|
||||
14200 1420 9.3701636e-05 0.00031517848 2270
|
||||
14400 1440 6.7389077e-05 0.0002946861 2270
|
||||
14600 1460 5.3640086e-05 0.00026650711 2270
|
||||
14800 1480 4.2699992e-05 0.00023789279 2270
|
||||
15000 1500 5.3012016e-05 0.00019933234 2270
|
||||
15200 1520 5.8834197e-05 0.00022407007 2270
|
||||
15400 1540 5.0899982e-05 0.00029695531 2270
|
||||
15600 1560 3.0476742e-05 0.00039119066 2270
|
||||
15800 1580 1.6633264e-05 0.00033770401 2270
|
||||
16000 1600 1.098906e-05 0.00036684894 2270
|
||||
16200 1620 1.464848e-05 0.00036449759 2270
|
||||
16400 1640 1.9598429e-05 0.00021056689 2270
|
||||
16600 1660 1.2644955e-05 0.00020781781 2270
|
||||
16800 1680 8.8428553e-06 0.000165 2270
|
||||
17000 1700 8.8971439e-06 0.00012266475 2270
|
||||
17200 1720 1.7032781e-05 0.00019873443 2270
|
||||
17400 1740 1.9448563e-05 0.00025661663 2270
|
||||
17600 1760 1.3714713e-05 0.000324022 2270
|
||||
17800 1780 9.1326468e-06 0.00031392513 2270
|
||||
18000 1800 9.2464802e-06 0.00029729527 2270
|
||||
18200 1820 1.5553042e-05 0.00027488475 2270
|
||||
18400 1840 1.4132933e-05 0.00019565459 2270
|
||||
18600 1860 9.4734832e-06 0.00016716988 2270
|
||||
18800 1880 5.5115145e-06 0.00013728033 2270
|
||||
19000 1900 8.268812e-06 0.00015119605 2270
|
||||
19200 1920 1.2470136e-05 0.00020222131 2270
|
||||
19400 1940 9.9387775e-06 0.00024503373 2270
|
||||
19600 1960 5.4241999e-06 0.00026921858 2270
|
||||
19800 1980 2.7987348e-06 0.00026201267 2270
|
||||
20000 2000 6.272538e-06 0.00025626323 2270
|
||||
20200 2020 8.0157781e-06 0.000220139 2270
|
||||
20400 2040 6.1652093e-06 0.00017089058 2270
|
||||
20600 2060 2.9967592e-06 0.00014582864 2270
|
||||
20800 2080 3.016678e-06 0.000148629 2270
|
||||
21000 2100 7.287645e-06 0.00016486102 2270
|
||||
21200 2120 8.6905277e-06 0.00020276916 2270
|
||||
21400 2140 6.8453018e-06 0.00023156153 2270
|
||||
21600 2160 3.3853799e-06 0.0002432462 2270
|
||||
21800 2180 4.1241209e-06 0.00022829024 2270
|
||||
22000 2200 7.0802396e-06 0.00020784823 2270
|
||||
22200 2220 7.3361691e-06 0.00018114134 2270
|
||||
22400 2240 5.0764593e-06 0.00014351106 2270
|
||||
22600 2260 2.7487537e-06 0.00012919872 2270
|
||||
22800 2280 4.620167e-06 0.00013746218 2270
|
||||
23000 2300 6.9819357e-06 0.00015985102 2270
|
||||
23200 2320 6.8923916e-06 0.00018713045 2270
|
||||
23400 2340 4.1795088e-06 0.00019846682 2270
|
||||
23600 2360 2.2871028e-06 0.00021068421 2270
|
||||
23800 2380 3.862046e-06 0.00019553306 2270
|
||||
24000 2400 5.2448555e-06 0.00017398041 2270
|
||||
24200 2420 4.7565441e-06 0.00015008142 2270
|
||||
24400 2440 2.2952135e-06 0.00012747106 2270
|
||||
24600 2460 2.1575617e-06 0.00012516996 2270
|
||||
24800 2480 4.1777868e-06 0.0001331902 2270
|
||||
25000 2500 5.5679133e-06 0.00015504562 2270
|
||||
25200 2520 4.5758741e-06 0.00017146032 2270
|
||||
25400 2540 2.3403277e-06 0.00017611666 2270
|
||||
25600 2560 2.7029302e-06 0.00016850788 2270
|
||||
25800 2580 4.3601102e-06 0.00015884642 2270
|
||||
26000 2600 5.2244249e-06 0.00013793898 2270
|
||||
26200 2620 3.4577672e-06 0.00012395875 2270
|
||||
26400 2640 2.361577e-06 0.00011600057 2270
|
||||
26600 2660 2.8515644e-06 0.00011277063 2270
|
||||
26800 2680 4.0851213e-06 0.0001290832 2270
|
||||
27000 2700 4.2579644e-06 0.0001476495 2270
|
||||
27200 2720 2.6593858e-06 0.00015977745 2270
|
||||
27400 2740 1.990115e-06 0.00015612787 2270
|
||||
27600 2760 2.6756835e-06 0.00014913772 2270
|
||||
27800 2780 3.9032806e-06 0.00014014763 2270
|
||||
28000 2800 3.2729446e-06 0.00012216846 2270
|
||||
28200 2820 1.9357278e-06 0.00011078621 2270
|
||||
28400 2840 1.7094832e-06 0.00010910509 2270
|
||||
28600 2860 2.8731406e-06 0.00011179644 2270
|
||||
28800 2880 3.7062354e-06 0.00012254091 2270
|
||||
29000 2900 2.7844262e-06 0.00013060331 2270
|
||||
29200 2920 1.7680655e-06 0.00013797514 2270
|
||||
29400 2940 1.706873e-06 0.0001350685 2270
|
||||
29600 2960 2.8764562e-06 0.00012428508 2270
|
||||
29800 2980 3.1502029e-06 0.00011456718 2270
|
||||
30000 3000 2.1833409e-06 0.00010317469 2270
|
||||
Loop time of 165.611 on 4 procs for 30000 steps with 2270 atoms
|
||||
|
||||
Performance: 1565111.240 tau/day, 181.147 timesteps/s, 411.204 katom-step/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 | 0.63183 | 21.226 | 42.266 | 444.6 | 12.82
|
||||
Bond | 0.095073 | 0.17799 | 0.27877 | 17.0 | 0.11
|
||||
Neigh | 2.0745 | 2.0781 | 2.0822 | 0.2 | 1.25
|
||||
Comm | 0.32024 | 0.38703 | 0.45564 | 8.1 | 0.23
|
||||
Output | 0.60459 | 0.76798 | 0.93724 | 18.6 | 0.46
|
||||
Modify | 119.85 | 140.76 | 161.36 | 172.2 | 85.00
|
||||
Other | | 0.2124 | | | 0.13
|
||||
|
||||
Nlocal: 567.5 ave 1139 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 75.5 ave 152 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 9238.25 ave 18490 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 17945 ave 35917 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 71780
|
||||
Ave neighs/atom = 31.621145
|
||||
Ave special neighs/atom = 0.22026432
|
||||
Neighbor list builds = 2071
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:02:45
|
||||
658
examples/rheo/ice-cubes/square.mol
Normal file
658
examples/rheo/ice-cubes/square.mol
Normal file
@ -0,0 +1,658 @@
|
||||
#Made with create_mol.py
|
||||
|
||||
100 atoms
|
||||
342 bonds
|
||||
|
||||
Coords
|
||||
#ID x y z
|
||||
1 -4 -4 0
|
||||
2 -3 -4 0
|
||||
3 -2 -4 0
|
||||
4 -1 -4 0
|
||||
5 0 -4 0
|
||||
6 1 -4 0
|
||||
7 2 -4 0
|
||||
8 3 -4 0
|
||||
9 4 -4 0
|
||||
10 5 -4 0
|
||||
11 -4 -3 0
|
||||
12 -3 -3 0
|
||||
13 -2 -3 0
|
||||
14 -1 -3 0
|
||||
15 0 -3 0
|
||||
16 1 -3 0
|
||||
17 2 -3 0
|
||||
18 3 -3 0
|
||||
19 4 -3 0
|
||||
20 5 -3 0
|
||||
21 -4 -2 0
|
||||
22 -3 -2 0
|
||||
23 -2 -2 0
|
||||
24 -1 -2 0
|
||||
25 0 -2 0
|
||||
26 1 -2 0
|
||||
27 2 -2 0
|
||||
28 3 -2 0
|
||||
29 4 -2 0
|
||||
30 5 -2 0
|
||||
31 -4 -1 0
|
||||
32 -3 -1 0
|
||||
33 -2 -1 0
|
||||
34 -1 -1 0
|
||||
35 0 -1 0
|
||||
36 1 -1 0
|
||||
37 2 -1 0
|
||||
38 3 -1 0
|
||||
39 4 -1 0
|
||||
40 5 -1 0
|
||||
41 -4 0 0
|
||||
42 -3 0 0
|
||||
43 -2 0 0
|
||||
44 -1 0 0
|
||||
45 0 0 0
|
||||
46 1 0 0
|
||||
47 2 0 0
|
||||
48 3 0 0
|
||||
49 4 0 0
|
||||
50 5 0 0
|
||||
51 -4 1 0
|
||||
52 -3 1 0
|
||||
53 -2 1 0
|
||||
54 -1 1 0
|
||||
55 0 1 0
|
||||
56 1 1 0
|
||||
57 2 1 0
|
||||
58 3 1 0
|
||||
59 4 1 0
|
||||
60 5 1 0
|
||||
61 -4 2 0
|
||||
62 -3 2 0
|
||||
63 -2 2 0
|
||||
64 -1 2 0
|
||||
65 0 2 0
|
||||
66 1 2 0
|
||||
67 2 2 0
|
||||
68 3 2 0
|
||||
69 4 2 0
|
||||
70 5 2 0
|
||||
71 -4 3 0
|
||||
72 -3 3 0
|
||||
73 -2 3 0
|
||||
74 -1 3 0
|
||||
75 0 3 0
|
||||
76 1 3 0
|
||||
77 2 3 0
|
||||
78 3 3 0
|
||||
79 4 3 0
|
||||
80 5 3 0
|
||||
81 -4 4 0
|
||||
82 -3 4 0
|
||||
83 -2 4 0
|
||||
84 -1 4 0
|
||||
85 0 4 0
|
||||
86 1 4 0
|
||||
87 2 4 0
|
||||
88 3 4 0
|
||||
89 4 4 0
|
||||
90 5 4 0
|
||||
91 -4 5 0
|
||||
92 -3 5 0
|
||||
93 -2 5 0
|
||||
94 -1 5 0
|
||||
95 0 5 0
|
||||
96 1 5 0
|
||||
97 2 5 0
|
||||
98 3 5 0
|
||||
99 4 5 0
|
||||
100 5 5 0
|
||||
|
||||
Types
|
||||
#ID type
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Masses
|
||||
#ID mass
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Bonds
|
||||
#ID type atom1 atom2
|
||||
1 1 1 2
|
||||
2 1 1 11
|
||||
3 1 1 12
|
||||
4 1 2 3
|
||||
5 1 2 11
|
||||
6 1 2 12
|
||||
7 1 2 13
|
||||
8 1 3 4
|
||||
9 1 3 12
|
||||
10 1 3 13
|
||||
11 1 3 14
|
||||
12 1 4 5
|
||||
13 1 4 13
|
||||
14 1 4 14
|
||||
15 1 4 15
|
||||
16 1 5 6
|
||||
17 1 5 14
|
||||
18 1 5 15
|
||||
19 1 5 16
|
||||
20 1 6 7
|
||||
21 1 6 15
|
||||
22 1 6 16
|
||||
23 1 6 17
|
||||
24 1 7 8
|
||||
25 1 7 16
|
||||
26 1 7 17
|
||||
27 1 7 18
|
||||
28 1 8 9
|
||||
29 1 8 17
|
||||
30 1 8 18
|
||||
31 1 8 19
|
||||
32 1 9 10
|
||||
33 1 9 18
|
||||
34 1 9 19
|
||||
35 1 9 20
|
||||
36 1 10 19
|
||||
37 1 10 20
|
||||
38 1 11 21
|
||||
39 1 11 12
|
||||
40 1 11 22
|
||||
41 1 12 21
|
||||
42 1 12 13
|
||||
43 1 12 22
|
||||
44 1 12 23
|
||||
45 1 13 22
|
||||
46 1 13 23
|
||||
47 1 13 14
|
||||
48 1 13 24
|
||||
49 1 14 23
|
||||
50 1 14 24
|
||||
51 1 14 15
|
||||
52 1 14 25
|
||||
53 1 15 24
|
||||
54 1 15 16
|
||||
55 1 15 25
|
||||
56 1 15 26
|
||||
57 1 16 25
|
||||
58 1 16 26
|
||||
59 1 16 17
|
||||
60 1 16 27
|
||||
61 1 17 26
|
||||
62 1 17 18
|
||||
63 1 17 27
|
||||
64 1 17 28
|
||||
65 1 18 27
|
||||
66 1 18 28
|
||||
67 1 18 19
|
||||
68 1 18 29
|
||||
69 1 19 28
|
||||
70 1 19 29
|
||||
71 1 19 20
|
||||
72 1 19 30
|
||||
73 1 20 29
|
||||
74 1 20 30
|
||||
75 1 21 22
|
||||
76 1 21 31
|
||||
77 1 21 32
|
||||
78 1 22 23
|
||||
79 1 22 31
|
||||
80 1 22 32
|
||||
81 1 22 33
|
||||
82 1 23 24
|
||||
83 1 23 32
|
||||
84 1 23 33
|
||||
85 1 23 34
|
||||
86 1 24 25
|
||||
87 1 24 33
|
||||
88 1 24 34
|
||||
89 1 24 35
|
||||
90 1 25 26
|
||||
91 1 25 34
|
||||
92 1 25 35
|
||||
93 1 25 36
|
||||
94 1 26 27
|
||||
95 1 26 35
|
||||
96 1 26 36
|
||||
97 1 26 37
|
||||
98 1 27 28
|
||||
99 1 27 36
|
||||
100 1 27 37
|
||||
101 1 27 38
|
||||
102 1 28 29
|
||||
103 1 28 37
|
||||
104 1 28 38
|
||||
105 1 28 39
|
||||
106 1 29 30
|
||||
107 1 29 38
|
||||
108 1 29 39
|
||||
109 1 29 40
|
||||
110 1 30 39
|
||||
111 1 30 40
|
||||
112 1 31 32
|
||||
113 1 31 41
|
||||
114 1 31 42
|
||||
115 1 32 33
|
||||
116 1 32 41
|
||||
117 1 32 42
|
||||
118 1 32 43
|
||||
119 1 33 34
|
||||
120 1 33 42
|
||||
121 1 33 43
|
||||
122 1 33 44
|
||||
123 1 34 35
|
||||
124 1 34 43
|
||||
125 1 34 44
|
||||
126 1 34 45
|
||||
127 1 35 36
|
||||
128 1 35 44
|
||||
129 1 35 45
|
||||
130 1 35 46
|
||||
131 1 36 37
|
||||
132 1 36 45
|
||||
133 1 36 46
|
||||
134 1 36 47
|
||||
135 1 37 38
|
||||
136 1 37 46
|
||||
137 1 37 47
|
||||
138 1 37 48
|
||||
139 1 38 39
|
||||
140 1 38 47
|
||||
141 1 38 48
|
||||
142 1 38 49
|
||||
143 1 39 40
|
||||
144 1 39 48
|
||||
145 1 39 49
|
||||
146 1 39 50
|
||||
147 1 40 49
|
||||
148 1 40 50
|
||||
149 1 41 51
|
||||
150 1 41 42
|
||||
151 1 41 52
|
||||
152 1 42 51
|
||||
153 1 42 43
|
||||
154 1 42 52
|
||||
155 1 42 53
|
||||
156 1 43 52
|
||||
157 1 43 53
|
||||
158 1 43 44
|
||||
159 1 43 54
|
||||
160 1 44 53
|
||||
161 1 44 54
|
||||
162 1 44 45
|
||||
163 1 44 55
|
||||
164 1 45 54
|
||||
165 1 45 46
|
||||
166 1 45 55
|
||||
167 1 45 56
|
||||
168 1 46 55
|
||||
169 1 46 56
|
||||
170 1 46 47
|
||||
171 1 46 57
|
||||
172 1 47 56
|
||||
173 1 47 48
|
||||
174 1 47 57
|
||||
175 1 47 58
|
||||
176 1 48 57
|
||||
177 1 48 58
|
||||
178 1 48 49
|
||||
179 1 48 59
|
||||
180 1 49 58
|
||||
181 1 49 59
|
||||
182 1 49 50
|
||||
183 1 49 60
|
||||
184 1 50 59
|
||||
185 1 50 60
|
||||
186 1 51 52
|
||||
187 1 51 61
|
||||
188 1 51 62
|
||||
189 1 52 53
|
||||
190 1 52 61
|
||||
191 1 52 62
|
||||
192 1 52 63
|
||||
193 1 53 54
|
||||
194 1 53 62
|
||||
195 1 53 63
|
||||
196 1 53 64
|
||||
197 1 54 55
|
||||
198 1 54 63
|
||||
199 1 54 64
|
||||
200 1 54 65
|
||||
201 1 55 56
|
||||
202 1 55 64
|
||||
203 1 55 65
|
||||
204 1 55 66
|
||||
205 1 56 57
|
||||
206 1 56 65
|
||||
207 1 56 66
|
||||
208 1 56 67
|
||||
209 1 57 58
|
||||
210 1 57 66
|
||||
211 1 57 67
|
||||
212 1 57 68
|
||||
213 1 58 59
|
||||
214 1 58 67
|
||||
215 1 58 68
|
||||
216 1 58 69
|
||||
217 1 59 60
|
||||
218 1 59 68
|
||||
219 1 59 69
|
||||
220 1 59 70
|
||||
221 1 60 69
|
||||
222 1 60 70
|
||||
223 1 61 71
|
||||
224 1 61 62
|
||||
225 1 61 72
|
||||
226 1 62 71
|
||||
227 1 62 63
|
||||
228 1 62 72
|
||||
229 1 62 73
|
||||
230 1 63 72
|
||||
231 1 63 73
|
||||
232 1 63 64
|
||||
233 1 63 74
|
||||
234 1 64 73
|
||||
235 1 64 74
|
||||
236 1 64 65
|
||||
237 1 64 75
|
||||
238 1 65 74
|
||||
239 1 65 66
|
||||
240 1 65 75
|
||||
241 1 65 76
|
||||
242 1 66 75
|
||||
243 1 66 76
|
||||
244 1 66 67
|
||||
245 1 66 77
|
||||
246 1 67 76
|
||||
247 1 67 68
|
||||
248 1 67 77
|
||||
249 1 67 78
|
||||
250 1 68 77
|
||||
251 1 68 78
|
||||
252 1 68 69
|
||||
253 1 68 79
|
||||
254 1 69 78
|
||||
255 1 69 79
|
||||
256 1 69 70
|
||||
257 1 69 80
|
||||
258 1 70 79
|
||||
259 1 70 80
|
||||
260 1 71 72
|
||||
261 1 71 81
|
||||
262 1 71 82
|
||||
263 1 72 73
|
||||
264 1 72 81
|
||||
265 1 72 82
|
||||
266 1 72 83
|
||||
267 1 73 74
|
||||
268 1 73 82
|
||||
269 1 73 83
|
||||
270 1 73 84
|
||||
271 1 74 75
|
||||
272 1 74 83
|
||||
273 1 74 84
|
||||
274 1 74 85
|
||||
275 1 75 76
|
||||
276 1 75 84
|
||||
277 1 75 85
|
||||
278 1 75 86
|
||||
279 1 76 77
|
||||
280 1 76 85
|
||||
281 1 76 86
|
||||
282 1 76 87
|
||||
283 1 77 78
|
||||
284 1 77 86
|
||||
285 1 77 87
|
||||
286 1 77 88
|
||||
287 1 78 79
|
||||
288 1 78 87
|
||||
289 1 78 88
|
||||
290 1 78 89
|
||||
291 1 79 80
|
||||
292 1 79 88
|
||||
293 1 79 89
|
||||
294 1 79 90
|
||||
295 1 80 89
|
||||
296 1 80 90
|
||||
297 1 81 82
|
||||
298 1 81 91
|
||||
299 1 81 92
|
||||
300 1 82 83
|
||||
301 1 82 91
|
||||
302 1 82 92
|
||||
303 1 82 93
|
||||
304 1 83 84
|
||||
305 1 83 92
|
||||
306 1 83 93
|
||||
307 1 83 94
|
||||
308 1 84 85
|
||||
309 1 84 93
|
||||
310 1 84 94
|
||||
311 1 84 95
|
||||
312 1 85 86
|
||||
313 1 85 94
|
||||
314 1 85 95
|
||||
315 1 85 96
|
||||
316 1 86 87
|
||||
317 1 86 95
|
||||
318 1 86 96
|
||||
319 1 86 97
|
||||
320 1 87 88
|
||||
321 1 87 96
|
||||
322 1 87 97
|
||||
323 1 87 98
|
||||
324 1 88 89
|
||||
325 1 88 97
|
||||
326 1 88 98
|
||||
327 1 88 99
|
||||
328 1 89 90
|
||||
329 1 89 98
|
||||
330 1 89 99
|
||||
331 1 89 100
|
||||
332 1 90 99
|
||||
333 1 90 100
|
||||
334 1 91 92
|
||||
335 1 92 93
|
||||
336 1 93 94
|
||||
337 1 94 95
|
||||
338 1 95 96
|
||||
339 1 96 97
|
||||
340 1 97 98
|
||||
341 1 98 99
|
||||
342 1 99 100
|
||||
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
@ -0,0 +1,102 @@
|
||||
# ------ 2D oxidizing bar ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -60 60 0 80 -0.01 0.01 units box
|
||||
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
|
||||
region lbar block -15 0 3 80 EDGE EDGE units box
|
||||
region rbar block 0 15 3 80 EDGE EDGE units box
|
||||
region bar union 2 lbar rbar
|
||||
region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
|
||||
|
||||
lattice hex 1.0
|
||||
create_atoms 1 region bar
|
||||
create_atoms 3 region floor
|
||||
|
||||
set region rbar type 2
|
||||
group bar type 1 2
|
||||
group rbar type 2
|
||||
group floor type 3
|
||||
|
||||
set group all sph/e 0.0
|
||||
set group all rheo/status 1
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.1*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 0.1
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
create_bonds many bar bar 1 0 1.5
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style hybrid bpm/spring rheo/shell t/form 100
|
||||
bond_coeff 1 bpm/spring 1.0 1.0 1.0
|
||||
bond_coeff 2 rheo/shell 0.2 0.2 0.1
|
||||
|
||||
# ------ Apply dynamics ------#
|
||||
|
||||
# Note: surface detection is not performed on solid bodies, so cannot use surface property
|
||||
compute coord all rheo/property/atom coordination
|
||||
variable surf atom c_coord<22
|
||||
group surf dynamic all var surf every 10
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
thermal &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} &
|
||||
specific/heat * constant ${Cv} &
|
||||
Tfreeze * constant ${Tf} &
|
||||
latent/heat * constant ${L} &
|
||||
react 1.5 1
|
||||
|
||||
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||
fix 8 floor setforce 0.0 0.0 0.0
|
||||
fix 9 surf add/heat linear 1.1 0.05
|
||||
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||
fix 11 all enforce2d
|
||||
|
||||
compute surf all rheo/property/atom surface
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond_shell all rheo/property/atom nbond/shell
|
||||
compute nbond_solid all nbond/atom bond/type 1
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf
|
||||
|
||||
run 40000
|
||||
488
examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4
Normal file
488
examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4
Normal file
@ -0,0 +1,488 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D oxidizing bar ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -60 60 0 80 -0.01 0.01 units box
|
||||
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region lbar block -15 0 3 80 EDGE EDGE units box
|
||||
region rbar block 0 15 3 80 EDGE EDGE units box
|
||||
region bar union 2 lbar rbar
|
||||
region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
|
||||
|
||||
lattice hex 1.0
|
||||
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||
create_atoms 1 region bar
|
||||
Created 2255 atoms
|
||||
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 3 region floor
|
||||
Created 446 atoms
|
||||
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set region rbar type 2
|
||||
Setting atom values ...
|
||||
1148 settings made for type
|
||||
group bar type 1 2
|
||||
2255 atoms in group bar
|
||||
group rbar type 2
|
||||
1148 atoms in group rbar
|
||||
group floor type 3
|
||||
446 atoms in group floor
|
||||
|
||||
set group all sph/e 0.0
|
||||
Setting atom values ...
|
||||
2701 settings made for sph/e
|
||||
set group all rheo/status 1
|
||||
Setting atom values ...
|
||||
2701 settings made for rheo/status
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.1*${rho0}/${mp}
|
||||
variable kappa equal 0.1*1/${mp}
|
||||
variable kappa equal 0.1*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 0.1
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
create_bonds many bar bar 1 0 1.5
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 73 49 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair rheo, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) pair rheo/solid, perpetual, trim from (2)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Added 6547 bonds, new total = 6547
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
6 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style hybrid bpm/spring rheo/shell t/form 100
|
||||
bond_coeff 1 bpm/spring 1.0 1.0 1.0
|
||||
bond_coeff 2 rheo/shell 0.2 0.2 0.1
|
||||
|
||||
# ------ Apply dynamics ------#
|
||||
|
||||
# Note: surface detection is not performed on solid bodies, so cannot use surface property
|
||||
compute coord all rheo/property/atom coordination
|
||||
variable surf atom c_coord<22
|
||||
group surf dynamic all var surf every 10
|
||||
dynamic group surf defined
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 0.1 react 1.5 1
|
||||
|
||||
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||
fix 8 floor setforce 0.0 0.0 0.0
|
||||
fix 9 surf add/heat linear 1.1 0.05
|
||||
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||
fix 11 all enforce2d
|
||||
|
||||
compute surf all rheo/property/atom surface
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute status all rheo/property/atom status
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond_shell all rheo/property/atom nbond/shell
|
||||
compute nbond_solid all nbond/atom bond/type 1
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status
|
||||
|
||||
run 40000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
- @article{ApplMathModel.130.310,
|
||||
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||
journal = {Applied Mathematical Modelling},
|
||||
volume = {130},
|
||||
pages = {310-326},
|
||||
year = {2024},
|
||||
issn = {0307-904X},
|
||||
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 73 49 1
|
||||
8 neighbor lists, perpetual/occasional/extra = 7 1 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (4)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) fix rheo/thermal, occasional, trim from (4)
|
||||
attributes: half, newton off, cut 3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(8) fix rheo/oxidation, perpetual, trim from (3)
|
||||
attributes: full, newton off, cut 1.8
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0 0 2701
|
||||
200 20 4.1743799e-07 1.1743617e-07 2701
|
||||
400 40 1.6697519e-06 4.6974469e-07 2701
|
||||
600 60 3.7127333e-06 1.0646825e-05 2701
|
||||
800 80 4.6683656e-06 0.00015182605 2701
|
||||
1000 100 4.7368707e-06 0.00028128761 2701
|
||||
1200 120 3.4384322e-06 0.00045913378 2701
|
||||
1400 140 1.4119866e-06 0.00055627091 2701
|
||||
1600 160 4.4114517e-07 0.00058247308 2701
|
||||
1800 180 4.8289229e-07 0.0005510948 2701
|
||||
2000 200 1.8494183e-06 0.00048386222 2701
|
||||
2200 220 3.3319816e-06 0.00037903264 2701
|
||||
2400 240 3.8128922e-06 0.00024115906 2701
|
||||
2600 260 3.1943401e-06 9.727407e-05 2701
|
||||
2800 280 1.6172816e-06 -2.632162e-05 2701
|
||||
3000 300 3.6100709e-07 -8.5761867e-05 2701
|
||||
3200 320 1.4745502e-07 -5.9204127e-05 2701
|
||||
3400 340 8.3369782e-07 8.8312464e-07 2701
|
||||
3600 360 2.0484052e-06 5.8521477e-05 2701
|
||||
3800 380 3.1639387e-06 0.0001685663 2701
|
||||
4000 400 3.1692907e-06 0.00026875988 2701
|
||||
4200 420 2.391933e-06 0.00038621787 2701
|
||||
4400 440 1.1964404e-06 0.00048901286 2701
|
||||
4600 460 4.0508824e-07 0.00051863639 2701
|
||||
4800 480 5.4908507e-07 0.00049263754 2701
|
||||
5000 500 1.3139665e-06 0.00041984264 2701
|
||||
5200 520 2.1939161e-06 0.00033095351 2701
|
||||
5400 540 2.3687031e-06 0.00022422981 2701
|
||||
5600 560 1.8280882e-06 0.00011544328 2701
|
||||
5800 580 8.8610517e-07 2.9307791e-05 2701
|
||||
6000 600 2.0989359e-07 -1.7340941e-05 2701
|
||||
6200 620 2.8658301e-07 -8.1237835e-06 2701
|
||||
6400 640 9.7636239e-07 4.3755922e-05 2701
|
||||
6600 660 1.891303e-06 0.0001185719 2701
|
||||
6800 680 2.4149904e-06 0.00020830273 2701
|
||||
7000 700 2.3174953e-06 0.00030114767 2701
|
||||
7200 720 1.7918612e-06 0.00037821537 2701
|
||||
7400 740 1.2114987e-06 0.0004233475 2701
|
||||
7600 760 9.9661553e-07 0.00042958263 2701
|
||||
7800 780 1.1552559e-06 0.00039944618 2701
|
||||
8000 800 1.5249138e-06 0.00034034478 2701
|
||||
8200 820 1.7453861e-06 0.00026826463 2701
|
||||
8400 840 1.6259021e-06 0.00019131768 2701
|
||||
8600 860 1.2612805e-06 0.0001162957 2701
|
||||
8800 880 8.6964518e-07 7.1771506e-05 2701
|
||||
9000 900 7.6892472e-07 5.6170687e-05 2701
|
||||
9200 920 1.0780045e-06 7.1925995e-05 2701
|
||||
9400 940 1.6514902e-06 0.00011635293 2701
|
||||
9600 960 2.1891377e-06 0.00017599885 2701
|
||||
9800 980 2.4551701e-06 0.00024127934 2701
|
||||
10000 1000 2.4277051e-06 0.00029918622 2701
|
||||
10200 1020 2.2655987e-06 0.00034067996 2701
|
||||
10400 1040 2.1767207e-06 0.00035598133 2701
|
||||
10600 1060 2.2796719e-06 0.00034359076 2701
|
||||
10800 1080 2.4884225e-06 0.00030749714 2701
|
||||
11000 1100 2.6387215e-06 0.00025725198 2701
|
||||
11200 1120 2.5968908e-06 0.00020170699 2701
|
||||
11400 1140 2.4108931e-06 0.00015185858 2701
|
||||
11600 1160 2.2375166e-06 0.00011800349 2701
|
||||
11800 1180 2.2407196e-06 0.00010646971 2701
|
||||
12000 1200 2.4845263e-06 0.00011817498 2701
|
||||
12200 1220 2.8733204e-06 0.00015013186 2701
|
||||
12400 1240 3.2437087e-06 0.00019211975 2701
|
||||
12600 1260 3.4732728e-06 0.00023620276 2701
|
||||
12800 1280 3.5836611e-06 0.00027352269 2701
|
||||
13000 1300 3.6592211e-06 0.00029533734 2701
|
||||
13200 1320 3.782506e-06 0.00030032559 2701
|
||||
13400 1340 3.9807086e-06 0.00028395722 2701
|
||||
13600 1360 4.2023176e-06 0.00025390325 2701
|
||||
13800 1380 4.3559781e-06 0.00021794236 2701
|
||||
14000 1400 4.4273371e-06 0.00018026034 2701
|
||||
14200 1420 4.49867e-06 0.0001526569 2701
|
||||
14400 1440 4.6591574e-06 0.00013707051 2701
|
||||
14600 1460 4.9589583e-06 0.00013803875 2701
|
||||
14800 1480 5.3859375e-06 0.00015455425 2701
|
||||
15000 1500 5.8639557e-06 0.00017954785 2701
|
||||
15200 1520 6.3075561e-06 0.0002084257 2701
|
||||
15400 1540 6.7022179e-06 0.0002347669 2701
|
||||
15600 1560 7.0789688e-06 0.00025020766 2701
|
||||
15800 1580 7.4734777e-06 0.00025394845 2701
|
||||
16000 1600 7.8884743e-06 0.00024571725 2701
|
||||
16200 1620 8.3224059e-06 0.00022706648 2701
|
||||
16400 1640 8.7337783e-06 0.00020320706 2701
|
||||
16600 1660 9.1454649e-06 0.00017824346 2701
|
||||
16800 1680 9.5948793e-06 0.00015961835 2701
|
||||
17000 1700 1.0106407e-05 0.00015135471 2701
|
||||
17200 1720 1.0707273e-05 0.00015166884 2701
|
||||
17400 1740 1.1392597e-05 0.0001645916 2701
|
||||
17600 1760 1.2118829e-05 0.00018119729 2701
|
||||
17800 1780 1.2846056e-05 0.0002003616 2701
|
||||
18000 1800 1.3555288e-05 0.00021585952 2701
|
||||
18200 1820 1.4301024e-05 0.00022290158 2701
|
||||
18400 1840 1.5089217e-05 0.00021970192 2701
|
||||
18600 1860 1.5902351e-05 0.00020911128 2701
|
||||
18800 1880 1.6753175e-05 0.00019278718 2701
|
||||
19000 1900 1.7602996e-05 0.00017584076 2701
|
||||
19200 1920 1.8479378e-05 0.00016206226 2701
|
||||
19400 1940 1.9421603e-05 0.00015575677 2701
|
||||
19600 1960 2.0477421e-05 0.00015687558 2701
|
||||
19800 1980 2.1617288e-05 0.00016424998 2701
|
||||
20000 2000 2.2814347e-05 0.00017466664 2701
|
||||
20200 2020 2.4029097e-05 0.00018647149 2701
|
||||
20400 2040 2.5255953e-05 0.00019516077 2701
|
||||
20600 2060 2.649418e-05 0.00019906384 2701
|
||||
20800 2080 2.7755897e-05 0.00019630586 2701
|
||||
21000 2100 2.9067854e-05 0.00018674721 2701
|
||||
21200 2120 3.0396477e-05 0.0001758048 2701
|
||||
21400 2140 3.1759719e-05 0.00016782801 2701
|
||||
21600 2160 3.3193597e-05 0.00016324138 2701
|
||||
21800 2180 3.4729384e-05 0.00016124274 2701
|
||||
22000 2200 3.6367594e-05 0.00016437457 2701
|
||||
22200 2220 3.8095131e-05 0.00017015573 2701
|
||||
22400 2240 3.9867003e-05 0.00017649465 2701
|
||||
22600 2260 4.169511e-05 0.00018111374 2701
|
||||
22800 2280 4.3566134e-05 0.00018104136 2701
|
||||
23000 2300 4.5461538e-05 0.00017822707 2701
|
||||
23200 2320 4.7377333e-05 0.00017285066 2701
|
||||
23400 2340 4.9354403e-05 0.00016826524 2701
|
||||
23600 2360 5.1399791e-05 0.00016517913 2701
|
||||
23800 2380 5.3510931e-05 0.00016299649 2701
|
||||
24000 2400 5.5681048e-05 0.00016256674 2701
|
||||
24200 2420 5.7902429e-05 0.00016513449 2701
|
||||
24400 2440 6.0216049e-05 0.00016895109 2701
|
||||
24600 2460 6.270982e-05 0.00016946227 2701
|
||||
24800 2480 6.5390117e-05 0.00016589426 2701
|
||||
25000 2500 6.8121899e-05 0.00016241676 2701
|
||||
25200 2520 7.0947331e-05 0.00015624292 2701
|
||||
25400 2540 7.4304148e-05 0.0001449537 2701
|
||||
25600 2560 7.7745077e-05 0.00013179658 2701
|
||||
25800 2580 8.0739829e-05 0.00013098838 2701
|
||||
26000 2600 8.3827874e-05 0.00014278841 2701
|
||||
26200 2620 8.7060677e-05 0.00015381649 2701
|
||||
26400 2640 9.0266508e-05 0.00016130999 2701
|
||||
26600 2660 9.3339049e-05 0.00016908268 2701
|
||||
26800 2680 9.6347013e-05 0.00016771087 2701
|
||||
27000 2700 9.9294711e-05 0.00016577315 2701
|
||||
27200 2720 0.00010230007 0.0001670893 2701
|
||||
27400 2740 0.00010547172 0.00016569077 2701
|
||||
27600 2760 0.00010872426 0.00016506303 2701
|
||||
27800 2780 0.00011201844 0.00016482702 2701
|
||||
28000 2800 0.00011532129 0.00016694886 2701
|
||||
28200 2820 0.00011869854 0.00016163005 2701
|
||||
28400 2840 0.00012209747 0.00015339281 2701
|
||||
28600 2860 0.00012549322 0.00014765883 2701
|
||||
28800 2880 0.00012898685 0.00014241765 2701
|
||||
29000 2900 0.00013259039 0.00014215724 2701
|
||||
29200 2920 0.00013628209 0.00014881155 2701
|
||||
29400 2940 0.00014001213 0.00015671333 2701
|
||||
29600 2960 0.00014379216 0.00016446215 2701
|
||||
29800 2980 0.00014764687 0.0001639602 2701
|
||||
30000 3000 0.00015142301 0.00015664816 2701
|
||||
30200 3020 0.00015496407 0.00015545099 2701
|
||||
30400 3040 0.00015797338 0.00015368625 2701
|
||||
30600 3060 0.00016042141 0.00015679918 2701
|
||||
30800 3080 0.00016244716 0.00016093678 2701
|
||||
31000 3100 0.00016202247 0.00016066954 2701
|
||||
31200 3120 0.0001613312 0.00015932059 2701
|
||||
31400 3140 0.00016274961 0.00015988567 2701
|
||||
31600 3160 0.00016541518 0.00015724809 2701
|
||||
31800 3180 0.00016809362 0.00015498827 2701
|
||||
32000 3200 0.00017067801 0.00014830489 2701
|
||||
32200 3220 0.00017333906 0.00014371345 2701
|
||||
32400 3240 0.0001759011 0.00014421259 2701
|
||||
32600 3260 0.00017849952 0.00014228443 2701
|
||||
32800 3280 0.00017801812 0.00014117391 2701
|
||||
33000 3300 0.00017718857 0.00014644675 2701
|
||||
33200 3320 0.00017833666 0.0001291286 2701
|
||||
33400 3340 0.000178576 0.00014878558 2701
|
||||
33600 3360 0.00017846711 0.00013905481 2701
|
||||
33800 3380 0.00017822937 0.00015535996 2701
|
||||
34000 3400 0.00017899663 0.00016094303 2701
|
||||
34200 3420 0.00017924661 0.00015017553 2701
|
||||
34400 3440 0.00018024855 0.00014723549 2701
|
||||
34600 3460 0.00018143865 0.00013903131 2701
|
||||
34800 3480 0.00018258173 0.00013722112 2701
|
||||
35000 3500 0.00018404873 0.00014675949 2701
|
||||
35200 3520 0.00018538521 0.00015108242 2701
|
||||
35400 3540 0.00018669649 0.00014564852 2701
|
||||
35600 3560 0.00018814608 0.00013762161 2701
|
||||
35800 3580 0.00018967415 0.00014602307 2701
|
||||
36000 3600 0.00019146735 0.000126909 2701
|
||||
36200 3620 0.00019414036 0.00012384379 2701
|
||||
36400 3640 0.00019613057 0.00011059573 2701
|
||||
36600 3660 0.00019897104 0.00013621801 2701
|
||||
36800 3680 0.00020169688 0.00013665462 2701
|
||||
37000 3700 0.00020447655 0.00013929258 2701
|
||||
37200 3720 0.00020711105 0.0001363895 2701
|
||||
37400 3740 0.00021077854 0.00013610672 2701
|
||||
37600 3760 0.00021303084 0.00015051235 2701
|
||||
37800 3780 0.00021619561 0.00012664801 2701
|
||||
38000 3800 0.0002194018 0.00012808247 2701
|
||||
38200 3820 0.00022242646 0.0001360174 2701
|
||||
38400 3840 0.00022531568 0.00013311221 2701
|
||||
38600 3860 0.00022821731 0.00013523939 2701
|
||||
38800 3880 0.000231228 0.00014090695 2701
|
||||
39000 3900 0.00023404038 0.00013661835 2701
|
||||
39200 3920 0.00023755044 0.00013659469 2701
|
||||
39400 3940 0.00024009059 0.00012097907 2701
|
||||
39600 3960 0.0002432098 9.7877876e-05 2701
|
||||
39800 3980 0.00024475294 0.0001164688 2701
|
||||
40000 4000 0.00024171274 0.00012432219 2701
|
||||
Loop time of 192.659 on 4 procs for 40000 steps with 2701 atoms
|
||||
|
||||
Performance: 1793840.118 tau/day, 207.620 timesteps/s, 560.783 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.881 | 24.402 | 30.74 | 114.6 | 12.67
|
||||
Bond | 1.1126 | 1.8917 | 2.6935 | 43.3 | 0.98
|
||||
Neigh | 35.387 | 35.508 | 35.625 | 1.5 | 18.43
|
||||
Comm | 1.5499 | 1.6694 | 1.8006 | 7.4 | 0.87
|
||||
Output | 0.99755 | 1.0072 | 1.0165 | 0.8 | 0.52
|
||||
Modify | 120.6 | 127.43 | 135.54 | 54.8 | 66.14
|
||||
Other | | 0.7553 | | | 0.39
|
||||
|
||||
Nlocal: 675.25 ave 1373 max 7 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 103 ave 163 max 50 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 10509 ave 21592 max 126 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 20367 ave 41981 max 141 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 81468
|
||||
Ave neighs/atom = 30.162162
|
||||
Ave special neighs/atom = 1.6593854
|
||||
Neighbor list builds = 39932
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:03:12
|
||||
75
examples/rheo/poiseuille/in.rheo.poiseuille
Normal file
75
examples/rheo/poiseuille/in.rheo.poiseuille
Normal file
@ -0,0 +1,75 @@
|
||||
# ------ 2D Poiseuille flow ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 20 -10 10 -0.01 0.01
|
||||
create_box 2 box
|
||||
lattice sq ${n}
|
||||
|
||||
region inner block INF INF -7.5 7.5 INF INF units box
|
||||
region walls block INF INF -7.5 7.5 INF INF units box side out
|
||||
|
||||
create_atoms 2 region walls
|
||||
create_atoms 1 region inner
|
||||
|
||||
group fluid type 1
|
||||
group rig type 2
|
||||
|
||||
displace_atoms fluid random 0.1 0.1 0 135414 units box
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 1.0
|
||||
variable kappa equal 1.0*${rho0}/${mp}
|
||||
variable fext equal 1e-4/${n}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable Dr equal 0.05*${cut}*${cs}
|
||||
|
||||
variable eta equal 0.1
|
||||
variable gd0 equal 5e-4
|
||||
variable npow equal 0.5
|
||||
variable K equal 0.001
|
||||
|
||||
mass * ${mp}
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/status 0
|
||||
set group rig rheo/status 1
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
#fix 2 all rheo/viscosity * power ${eta} ${gd0} ${K} ${npow}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 rig setforce 0.0 0.0 0.0
|
||||
fix 5 fluid addforce ${fext} 0.0 0.0
|
||||
fix 6 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 20000
|
||||
|
||||
288
examples/rheo/poiseuille/log.17Apr2024.poiseuille.g++.4
Normal file
288
examples/rheo/poiseuille/log.17Apr2024.poiseuille.g++.4
Normal file
@ -0,0 +1,288 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D Poiseuille flow ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 20 -10 10 -0.01 0.01
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
lattice sq ${n}
|
||||
lattice sq 1
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
|
||||
region inner block INF INF -7.5 7.5 INF INF units box
|
||||
region walls block INF INF -7.5 7.5 INF INF units box side out
|
||||
|
||||
create_atoms 2 region walls
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 region inner
|
||||
Created 300 atoms
|
||||
using lattice units in orthogonal box = (0 -10 -0.01) to (20 10 0.01)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
group fluid type 1
|
||||
300 atoms in group fluid
|
||||
group rig type 2
|
||||
100 atoms in group rig
|
||||
|
||||
displace_atoms fluid random 0.1 0.1 0 135414 units box
|
||||
Displacing atoms ...
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 1.0
|
||||
variable kappa equal 1.0*${rho0}/${mp}
|
||||
variable kappa equal 1.0*1/${mp}
|
||||
variable kappa equal 1.0*1/1
|
||||
variable fext equal 1e-4/${n}
|
||||
variable fext equal 1e-4/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable Dr equal 0.05*${cut}*${cs}
|
||||
variable Dr equal 0.05*3*${cs}
|
||||
variable Dr equal 0.05*3*1
|
||||
|
||||
variable eta equal 0.1
|
||||
variable gd0 equal 5e-4
|
||||
variable npow equal 0.5
|
||||
variable K equal 0.001
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/rho 1
|
||||
Setting atom values ...
|
||||
400 settings made for rheo/rho
|
||||
set group all rheo/status 0
|
||||
Setting atom values ...
|
||||
400 settings made for rheo/status
|
||||
set group rig rheo/status 1
|
||||
Setting atom values ...
|
||||
100 settings made for rheo/status
|
||||
|
||||
timestep ${dt_max}
|
||||
timestep 0.1
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp 0.15
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift
|
||||
fix 1 all rheo 3 quintic 0 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.1
|
||||
#fix 2 all rheo/viscosity * power ${eta} ${gd0} ${K} ${npow}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 rig setforce 0.0 0.0 0.0
|
||||
fix 5 fluid addforce ${fext} 0.0 0.0
|
||||
fix 5 fluid addforce 0.0001 0.0 0.0
|
||||
fix 6 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 20000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 13 13 1
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair rheo, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.693 | 5.693 | 5.693 Mbytes
|
||||
Step Time KinEng Press
|
||||
0 0 0 0
|
||||
200 20 1.2220462e-06 3.7383146e-05
|
||||
400 40 4.345762e-06 7.5866885e-05
|
||||
600 60 8.8559433e-06 0.00011353743
|
||||
800 80 1.4370506e-05 0.00015135634
|
||||
1000 100 2.0576198e-05 0.00018903722
|
||||
1200 120 2.721926e-05 0.00022533997
|
||||
1400 140 3.4099653e-05 0.00026016069
|
||||
1600 160 4.1064175e-05 0.00029445207
|
||||
1800 180 4.8001225e-05 0.00032893763
|
||||
2000 200 5.4832849e-05 0.00036402396
|
||||
2200 220 6.1508431e-05 0.00039945249
|
||||
2400 240 6.8000141e-05 0.00043534411
|
||||
2600 260 7.430136e-05 0.00046943441
|
||||
2800 280 8.0415328e-05 0.00049807225
|
||||
3000 300 8.6335032e-05 0.00051815375
|
||||
3200 320 9.2021626e-05 0.00052618224
|
||||
3400 340 9.7387936e-05 0.00051877918
|
||||
3600 360 0.00010231526 0.00048650828
|
||||
3800 380 0.00010676617 0.00044578079
|
||||
4000 400 0.00011080098 0.00044777126
|
||||
4200 420 0.00011448127 0.00047047629
|
||||
4400 440 0.00011787852 0.00050280249
|
||||
4600 460 0.00012106805 0.0005397213
|
||||
4800 480 0.00012412056 0.00057885539
|
||||
5000 500 0.0001271078 0.00061396896
|
||||
5200 520 0.00013006637 0.00063981812
|
||||
5400 540 0.00013295039 0.00065094073
|
||||
5600 560 0.00013561487 0.00063918847
|
||||
5800 580 0.00013791796 0.00059087656
|
||||
6000 600 0.00013983422 0.00052171998
|
||||
6200 620 0.00014144833 0.00050658002
|
||||
6400 640 0.00014286538 0.0005248626
|
||||
6600 660 0.00014417734 0.00055826606
|
||||
6800 680 0.00014546931 0.00060063748
|
||||
7000 700 0.00014682553 0.00064421411
|
||||
7200 720 0.0001482833 0.00068252242
|
||||
7400 740 0.00014977996 0.00070671308
|
||||
7600 760 0.00015114829 0.00069774026
|
||||
7800 780 0.0001522719 0.00064408311
|
||||
8000 800 0.00015312897 0.00055977044
|
||||
8200 820 0.00015375669 0.0005225573
|
||||
8400 840 0.00015425683 0.00053833691
|
||||
8600 860 0.00015471278 0.00057447427
|
||||
8800 880 0.0001552059 0.00061980921
|
||||
9000 900 0.00015581593 0.0006659836
|
||||
9200 920 0.0001565564 0.00070813532
|
||||
9400 940 0.00015733573 0.00073378551
|
||||
9600 960 0.00015802107 0.00071560835
|
||||
9800 980 0.00015855339 0.00065636189
|
||||
10000 1000 0.00015890743 0.0005699855
|
||||
10200 1020 0.00015908095 0.00053138971
|
||||
10400 1040 0.00015915523 0.00054790708
|
||||
10600 1060 0.00015921254 0.00058899454
|
||||
10800 1080 0.00015934193 0.00063964906
|
||||
11000 1100 0.00015959891 0.00069241358
|
||||
11200 1120 0.0001599636 0.00073734651
|
||||
11400 1140 0.00016036526 0.00074477329
|
||||
11600 1160 0.00016075471 0.00071047555
|
||||
11800 1180 0.00016109516 0.00064173183
|
||||
12000 1200 0.00016131524 0.00055500553
|
||||
12200 1220 0.00016136366 0.0005290215
|
||||
12400 1240 0.0001613025 0.00055124296
|
||||
12600 1260 0.00016123023 0.00059758627
|
||||
12800 1280 0.00016123043 0.00065488735
|
||||
13000 1300 0.00016132935 0.0007140876
|
||||
13200 1320 0.00016152165 0.00074795629
|
||||
13400 1340 0.00016180372 0.00074730778
|
||||
13600 1360 0.00016216585 0.00071370995
|
||||
13800 1380 0.0001625339 0.00065176323
|
||||
14000 1400 0.00016274999 0.00057515371
|
||||
14200 1420 0.00016271295 0.00055878258
|
||||
14400 1440 0.00016249768 0.00058448193
|
||||
14600 1460 0.00016223675 0.00063096229
|
||||
14800 1480 0.00016201846 0.00068639548
|
||||
15000 1500 0.00016190593 0.00072444357
|
||||
15200 1520 0.00016194466 0.00073830636
|
||||
15400 1540 0.00016216164 0.00072773256
|
||||
15600 1560 0.00016253174 0.00069215481
|
||||
15800 1580 0.00016290895 0.00063239408
|
||||
16000 1600 0.00016306463 0.00057466273
|
||||
16200 1620 0.00016292218 0.00057951567
|
||||
16400 1640 0.00016261117 0.00061504156
|
||||
16600 1660 0.00016225906 0.00066066637
|
||||
16800 1680 0.00016197993 0.00069751908
|
||||
17000 1700 0.0001618568 0.00072202303
|
||||
17200 1720 0.00016194264 0.00073255034
|
||||
17400 1740 0.00016225911 0.0007231031
|
||||
17600 1760 0.00016270465 0.00068931224
|
||||
17800 1780 0.00016304053 0.00062934836
|
||||
18000 1800 0.00016302624 0.00058060272
|
||||
18200 1820 0.00016274847 0.00058859513
|
||||
18400 1840 0.00016236893 0.00061804803
|
||||
18600 1860 0.00016202777 0.00065393237
|
||||
18800 1880 0.0001618184 0.00068747094
|
||||
19000 1900 0.0001618044 0.00071352541
|
||||
19200 1920 0.00016204402 0.00072351769
|
||||
19400 1940 0.00016249999 0.00071330322
|
||||
19600 1960 0.00016297924 0.00067984167
|
||||
19800 1980 0.00016317435 0.00061634142
|
||||
20000 2000 0.00016301186 0.00057234115
|
||||
Loop time of 15.6198 on 4 procs for 20000 steps with 400 atoms
|
||||
|
||||
Performance: 11062881.511 tau/day, 1280.426 timesteps/s, 512.170 katom-step/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 | 2.1979 | 2.4473 | 2.6992 | 15.7 | 15.67
|
||||
Neigh | 0.024709 | 0.027006 | 0.029223 | 1.3 | 0.17
|
||||
Comm | 0.4657 | 0.71686 | 0.9662 | 29.0 | 4.59
|
||||
Output | 0.033698 | 0.036781 | 0.039359 | 1.1 | 0.24
|
||||
Modify | 12.306 | 12.313 | 12.319 | 0.2 | 78.83
|
||||
Other | | 0.07916 | | | 0.51
|
||||
|
||||
Nlocal: 100 ave 107 max 93 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 185.5 ave 192 max 179 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1712 ave 1848 max 1598 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
FullNghs: 3424 ave 3682 max 3174 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 13696
|
||||
Ave neighs/atom = 34.24
|
||||
Neighbor list builds = 331
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:15
|
||||
65
examples/rheo/taylor-green/in.rheo.taylor.green
Normal file
65
examples/rheo/taylor-green/in.rheo.taylor.green
Normal file
@ -0,0 +1,65 @@
|
||||
# ------ 2D Taylor Green vortex ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 40 0 40 -0.01 0.01
|
||||
create_box 1 box
|
||||
lattice sq ${n}
|
||||
|
||||
create_atoms 1 region box
|
||||
|
||||
displace_atoms all random 0.1 0.1 0 135414 units box
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable cs equal 1.0
|
||||
variable eta equal 0.05
|
||||
variable zeta equal 1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable Dr equal 0.1*${cut}*${cs}
|
||||
|
||||
mass * ${mp}
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/status 0
|
||||
|
||||
variable u0 equal 0.05
|
||||
variable uy atom ${u0}*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||
variable ux atom -${u0}*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||
variable d0 atom ${rho0}-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
|
||||
velocity all set v_ux v_uy 0.0 units box
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} RK1 8 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 10000
|
||||
224
examples/rheo/taylor-green/log.17Apr2024.taylor.green.g++.4
Normal file
224
examples/rheo/taylor-green/log.17Apr2024.taylor.green.g++.4
Normal file
@ -0,0 +1,224 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D Taylor Green vortex ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary p p p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 3.0
|
||||
|
||||
region box block 0 40 0 40 -0.01 0.01
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.01) to (40 40 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
lattice sq ${n}
|
||||
lattice sq 1
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
|
||||
create_atoms 1 region box
|
||||
Created 1600 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.01) to (40 40 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
displace_atoms all random 0.1 0.1 0 135414 units box
|
||||
Displacing atoms ...
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable cs equal 1.0
|
||||
variable eta equal 0.05
|
||||
variable zeta equal 1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable Dr equal 0.1*${cut}*${cs}
|
||||
variable Dr equal 0.1*3*${cs}
|
||||
variable Dr equal 0.1*3*1
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
set group all rheo/rho ${rho0}
|
||||
set group all rheo/rho 1
|
||||
Setting atom values ...
|
||||
1600 settings made for rheo/rho
|
||||
set group all rheo/status 0
|
||||
Setting atom values ...
|
||||
1600 settings made for rheo/status
|
||||
|
||||
variable u0 equal 0.05
|
||||
variable uy atom ${u0}*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||
variable uy atom 0.05*sin(2*PI*x/lx)*cos(2*PI*y/ly)
|
||||
variable ux atom -${u0}*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||
variable ux atom -0.05*sin(2*PI*y/ly)*cos(2*PI*x/ly)
|
||||
variable d0 atom ${rho0}-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-${u0}*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*${u0}*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*0.05*${rho0}*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/${cs}/${cs}
|
||||
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/${cs}
|
||||
variable d0 atom 1-0.05*0.05*1*0.25*(cos(4*PI*x/lx)+cos(4*PI*y/ly))/1/1
|
||||
|
||||
velocity all set v_ux v_uy 0.0 units box
|
||||
|
||||
timestep ${dt_max}
|
||||
timestep 0.1
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc ${zeta} rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp ${Dr}
|
||||
pair_style rheo 3 artificial/visc 1 rho/damp 0.3
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} RK1 8 shift
|
||||
fix 1 all rheo 3 RK1 8 shift
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 25 25 1
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair rheo, perpetual, half/full from (2)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.835 | 6.835 | 6.835 Mbytes
|
||||
Step Time KinEng Press
|
||||
0 0 0.00062497276 0.00062607301
|
||||
200 20 0.00056200647 0.00056633785
|
||||
400 40 0.00050570968 0.00051098771
|
||||
600 60 0.00045586684 0.00046081672
|
||||
800 80 0.00041124523 0.00041549607
|
||||
1000 100 0.00037065341 0.00037412741
|
||||
1200 120 0.00033391585 0.00033580899
|
||||
1400 140 0.00030078316 0.00030057307
|
||||
1600 160 0.00027093231 0.00026842603
|
||||
1800 180 0.00024403239 0.00023839026
|
||||
2000 200 0.0002197865 0.00021148941
|
||||
2200 220 0.0001979269 0.00018659386
|
||||
2400 240 0.00017822267 0.00016430442
|
||||
2600 260 0.00016047141 0.00014408514
|
||||
2800 280 0.00014448504 0.00012574125
|
||||
3000 300 0.00013009159 0.00010869938
|
||||
3200 320 0.00011713578 9.414951e-05
|
||||
3400 340 0.00010547564 8.1900579e-05
|
||||
3600 360 9.4982139e-05 7.1285649e-05
|
||||
3800 380 8.5538983e-05 6.1571123e-05
|
||||
4000 400 7.7040171e-05 5.3462572e-05
|
||||
4200 420 6.9390317e-05 4.6338308e-05
|
||||
4400 440 6.2503763e-05 3.9697323e-05
|
||||
4600 460 5.6303766e-05 3.4234465e-05
|
||||
4800 480 5.0721595e-05 3.0841338e-05
|
||||
5000 500 4.5695301e-05 2.7788566e-05
|
||||
5200 520 4.1169161e-05 2.5744409e-05
|
||||
5400 540 3.7093059e-05 2.3912739e-05
|
||||
5600 560 3.3421819e-05 2.2494185e-05
|
||||
5800 580 3.0114735e-05 2.1594384e-05
|
||||
6000 600 2.7135224e-05 2.1164421e-05
|
||||
6200 620 2.4450446e-05 2.0979349e-05
|
||||
6400 640 2.2030925e-05 2.0858567e-05
|
||||
6600 660 1.9850196e-05 2.098115e-05
|
||||
6800 680 1.7884553e-05 2.1134827e-05
|
||||
7000 700 1.6112763e-05 2.1242242e-05
|
||||
7200 720 1.4515783e-05 2.1312763e-05
|
||||
7400 740 1.3076456e-05 2.1370947e-05
|
||||
7600 760 1.1779327e-05 2.1332126e-05
|
||||
7800 780 1.0610469e-05 2.1156562e-05
|
||||
8000 800 9.5573298e-06 2.0898126e-05
|
||||
8200 820 8.6085799e-06 2.0517958e-05
|
||||
8400 840 7.7539888e-06 1.9841551e-05
|
||||
8600 860 6.9843033e-06 1.9114769e-05
|
||||
8800 880 6.2911575e-06 1.8362959e-05
|
||||
9000 900 5.6669785e-06 1.7473404e-05
|
||||
9200 920 5.1049208e-06 1.6452745e-05
|
||||
9400 940 4.5987908e-06 1.5578629e-05
|
||||
9600 960 4.1429972e-06 1.4427274e-05
|
||||
9800 980 3.7324962e-06 1.3169649e-05
|
||||
10000 1000 3.3627455e-06 1.1938723e-05
|
||||
Loop time of 38.2006 on 4 procs for 10000 steps with 1600 atoms
|
||||
|
||||
Performance: 2261743.875 tau/day, 261.776 timesteps/s, 418.841 katom-step/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 | 8.2958 | 8.7273 | 9.3582 | 15.2 | 22.85
|
||||
Neigh | 0.034282 | 0.035689 | 0.037115 | 0.7 | 0.09
|
||||
Comm | 0.16788 | 0.17018 | 0.17278 | 0.4 | 0.45
|
||||
Output | 0.066977 | 0.06882 | 0.071704 | 0.7 | 0.18
|
||||
Modify | 28.483 | 28.793 | 28.962 | 3.6 | 75.37
|
||||
Other | | 0.4053 | | | 1.06
|
||||
|
||||
Nlocal: 400 ave 402 max 399 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 307.25 ave 308 max 305 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 7618.25 ave 7697 max 7564 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
FullNghs: 13343 ave 13497 max 13258 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 53372
|
||||
Ave neighs/atom = 33.3575
|
||||
Neighbor list builds = 123
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:38
|
||||
Reference in New Issue
Block a user