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