190 lines
8.5 KiB
Groff
190 lines
8.5 KiB
Groff
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
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using 1 OpenMP thread(s) per MPI task
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# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
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units lj
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atom_style line
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dimension 2
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read_data data.line
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Reading data file ...
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orthogonal box = (-22.553882 -22.553882 -0.5) to (22.553882 22.553882 0.5)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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350 atoms
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350 lines
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read_data CPU = 0.003 seconds
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velocity all create 1.44 320984 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude molecule/intra all
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pair_style line/lj 2.5
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pair_coeff * * 0.25 0.25 1.0 0.25 2.5
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fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983
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100 rigid bodies with 350 atoms
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fix 3 all deform 5 x scale 0.8 y scale 0.8
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fix 4 all enforce2d
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compute 10 all property/atom end1x end1y end2x end2y
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#dump 1 all custom 500 dump1.atom id type x y z ix iy iz
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#dump 2 all custom 500 dump1.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
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timestep 0.001
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compute 1 all erotate/asphere
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compute 2 all ke
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compute 3 all pe
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variable toteng equal (c_1+c_2+c_3)/atoms
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compute_modify thermo_temp extra/dof -350
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thermo 1000
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thermo_style custom step f_2 pe ke c_1 c_2 c_3 v_toteng
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282–-3297}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 33 33 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair line/lj, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.742 | 4.742 | 4.742 Mbytes
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Step f_2 PotEng KinEng c_1 c_2 c_3 v_toteng
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0 1.1872976 0 0.46543528 0.03617212 0.46543528 0 0.5016074
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1000 1.9084412 -0.001043719 0.71003395 0.089891202 0.71003395 -0.001043719 0.79888143
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2000 2.31668 -0.020711665 0.83611544 0.13062287 0.83611544 -0.020711665 0.94602664
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3000 2.3094506 -0.062018072 0.80584123 0.15326943 0.80584123 -0.062018072 0.8970926
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4000 2.4383442 -0.053659995 0.86864073 0.14696993 0.86864073 -0.053659995 0.96195067
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5000 2.5885917 -0.15612821 0.90351683 0.17156633 0.90351683 -0.15612821 0.91895495
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6000 2.1187379 -0.072041135 0.76933527 0.11557939 0.76933527 -0.072041135 0.81287353
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7000 2.1407592 -0.057727294 0.75154343 0.13827066 0.75154343 -0.057727294 0.8320868
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8000 2.0661844 -0.097529608 0.71093839 0.14547433 0.71093839 -0.097529608 0.75888311
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9000 2.1574445 -0.052890857 0.78826145 0.11363136 0.78826145 -0.052890857 0.84900195
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10000 2.473097 -0.092376489 0.85756337 0.16861278 0.85756337 -0.092376489 0.93379965
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Loop time of 1.16704 on 1 procs for 10000 steps with 350 atoms
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Performance: 740334.372 tau/day, 8568.685 timesteps/s, 2.999 Matom-step/s
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99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.80757 | 0.80757 | 0.80757 | 0.0 | 69.20
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Neigh | 0.0090046 | 0.0090046 | 0.0090046 | 0.0 | 0.77
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Comm | 0.011808 | 0.011808 | 0.011808 | 0.0 | 1.01
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Output | 0.000194 | 0.000194 | 0.000194 | 0.0 | 0.02
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Modify | 0.3317 | 0.3317 | 0.3317 | 0.0 | 28.42
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Other | | 0.006768 | | | 0.58
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Nlocal: 350 ave 350 max 350 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 101 ave 101 max 101 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 853 ave 853 max 853 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 853
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Ave neighs/atom = 2.4371429
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Neighbor list builds = 274
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Dangerous builds = 0
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#undump 1
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#undump 2
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unfix 3
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change_box all triclinic
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Changing box ...
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triclinic box = (-18.043106 -18.043106 -0.5) to (18.043106 18.043106 0.5) with tilt (0 0 0)
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#dump 1 all custom 500 dump2.atom id type x y z ix iy iz
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#dump 2 all custom 500 dump2.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
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fix 3 all deform 1 xy erate 0.01 units box
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run 10000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 26 26 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair line/lj, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton/tri
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stencil: half/bin/2d/tri
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.756 | 4.756 | 4.756 Mbytes
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Step f_2 PotEng KinEng c_1 c_2 c_3 v_toteng
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10000 2.473097 -0.092380532 0.85753671 0.16863499 0.85753671 -0.092380532 0.93379117
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11000 2.5185915 -0.1015737 0.84230876 0.197573 0.84230876 -0.1015737 0.93830806
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12000 2.5971728 -0.13087195 0.90608898 0.17248755 0.90608898 -0.13087195 0.94770458
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13000 2.5065714 -0.14666584 0.83804307 0.19683483 0.83804307 -0.14666584 0.88821206
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14000 2.1672357 -0.10720878 0.79713452 0.10973398 0.79713452 -0.10720878 0.79965972
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15000 2.3444438 -0.14780285 0.81642139 0.15695019 0.81642139 -0.14780285 0.82556873
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16000 2.2672973 -0.12590007 0.76672668 0.17081014 0.76672668 -0.12590007 0.81163675
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17000 2.3999651 -0.15464102 0.85708567 0.14289234 0.85708567 -0.15464102 0.84533699
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18000 2.2024356 -0.14077779 0.76727873 0.14718521 0.76727873 -0.14077779 0.77368615
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19000 2.5411572 -0.092014576 0.85750101 0.19297197 0.85750101 -0.092014576 0.95845841
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20000 2.2113691 -0.11944862 0.77295445 0.14564597 0.77295445 -0.11944862 0.79915181
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Loop time of 1.76388 on 1 procs for 10000 steps with 350 atoms
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Performance: 489827.896 tau/day, 5669.304 timesteps/s, 1.984 Matom-step/s
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.3668 | 1.3668 | 1.3668 | 0.0 | 77.49
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Neigh | 0.018849 | 0.018849 | 0.018849 | 0.0 | 1.07
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Comm | 0.013338 | 0.013338 | 0.013338 | 0.0 | 0.76
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Output | 0.00020434 | 0.00020434 | 0.00020434 | 0.0 | 0.01
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Modify | 0.35698 | 0.35698 | 0.35698 | 0.0 | 20.24
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Other | | 0.007667 | | | 0.43
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Nlocal: 350 ave 350 max 350 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 119 ave 119 max 119 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 997 ave 997 max 997 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 997
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Ave neighs/atom = 2.8485714
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Neighbor list builds = 283
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Dangerous builds = 0
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Total wall time: 0:00:02
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