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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2 by 2 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) = 4.736 | 4.736 | 4.736 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 0.91895494
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6000 2.118738 -0.072041141 0.76933528 0.1155794 0.76933528 -0.072041141 0.81287354
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7000 2.1407609 -0.057727453 0.75154404 0.13827078 0.75154404 -0.057727453 0.83208737
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8000 2.066348 -0.097639137 0.71096217 0.14551295 0.71096217 -0.097639137 0.75883597
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9000 2.1969096 -0.050133795 0.8028133 0.11559948 0.8028133 -0.050133795 0.86827899
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10000 2.3932442 -0.098008752 0.83753779 0.15678193 0.83753779 -0.098008752 0.89631097
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Loop time of 0.596624 on 4 procs for 10000 steps with 350 atoms
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Performance: 1448149.372 tau/day, 16760.988 timesteps/s, 5.866 Matom-step/s
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98.2% CPU use with 4 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 | 0.17419 | 0.21073 | 0.27006 | 7.8 | 35.32
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Neigh | 0.0015899 | 0.0018079 | 0.0020932 | 0.5 | 0.30
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Comm | 0.041688 | 0.101 | 0.13805 | 11.3 | 16.93
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Output | 0.00011945 | 0.0001262 | 0.000143 | 0.0 | 0.02
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Modify | 0.26906 | 0.27183 | 0.27467 | 0.4 | 45.56
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Other | | 0.01113 | | | 1.87
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Nlocal: 87.5 ave 94 max 80 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 54.5 ave 67 max 42 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 212.75 ave 286 max 122 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Total # of neighbors = 851
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Ave neighs/atom = 2.4314286
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Neighbor list builds = 273
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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) = 4.752 | 4.752 | 4.752 Mbytes
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Step f_2 PotEng KinEng c_1 c_2 c_3 v_toteng
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10000 2.3932442 -0.098029446 0.83751359 0.1568021 0.83751359 -0.098029446 0.89628624
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11000 2.4541893 -0.15538223 0.82053681 0.19271549 0.82053681 -0.15538223 0.85787007
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12000 2.4124449 -0.14024177 0.84559598 0.15692416 0.84559598 -0.14024177 0.86227837
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13000 2.2095814 -0.10822636 0.73930104 0.173052 0.73930104 -0.10822636 0.80412668
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14000 2.0946831 -0.087303541 0.77743494 0.10023865 0.77743494 -0.087303541 0.79037005
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15000 2.0911016 -0.11524594 0.74044758 0.12978235 0.74044758 -0.11524594 0.75498398
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16000 1.9736428 -0.17259563 0.67852978 0.13943094 0.67852978 -0.17259563 0.64536509
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17000 2.3284367 -0.17673537 0.77018991 0.1897596 0.77018991 -0.17673537 0.78321414
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18000 2.3178564 -0.16634746 0.81488323 0.1487365 0.81488323 -0.16634746 0.79727227
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19000 2.7497251 -0.18254513 1.0041125 0.14528424 1.0041125 -0.18254513 0.96685165
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20000 2.3897059 -0.12664177 0.8390411 0.15426546 0.8390411 -0.12664177 0.86666479
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Loop time of 0.79519 on 4 procs for 10000 steps with 350 atoms
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Performance: 1086533.223 tau/day, 12575.616 timesteps/s, 4.401 Matom-step/s
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98.2% CPU use with 4 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 | 0.26601 | 0.35051 | 0.443 | 12.3 | 44.08
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Neigh | 0.0029891 | 0.0036725 | 0.0040631 | 0.7 | 0.46
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Comm | 0.049744 | 0.14268 | 0.22734 | 19.3 | 17.94
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Output | 0.00013783 | 0.00014503 | 0.00016304 | 0.0 | 0.02
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Modify | 0.27963 | 0.28446 | 0.29049 | 0.8 | 35.77
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Other | | 0.01372 | | | 1.73
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Nlocal: 87.5 ave 101 max 75 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Nghost: 61.5 ave 67 max 50 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Neighs: 244.75 ave 268 max 198 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Total # of neighbors = 979
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Ave neighs/atom = 2.7971429
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Neighbor list builds = 289
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Dangerous builds = 0
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Total wall time: 0:00:01
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