142 lines
5.8 KiB
Groff
142 lines
5.8 KiB
Groff
LAMMPS (22 Sep 2017)
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using 1 OpenMP thread(s) per MPI task
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units lj
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dimension 3
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boundary p p p
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atom_style atomic
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# truncated and shifted LJ potential
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pair_style lj/cut 2.5
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pair_modify shift yes
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# fcc lattice
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lattice fcc 0.9731
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Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
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region my_box block 0 8.0 0 8.0 0 20.0
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create_box 1 my_box
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Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
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1 by 1 by 1 MPI processor grid
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region particles block 0 8.0 0 8.0 0 20.0
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create_atoms 1 region particles
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Created 5120 atoms
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pair_coeff 1 1 1.0 1.0 2.5
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mass 1 1.0
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change_box all z final 0.0 34 remap units box
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orthogonal box = (0 0 0) to (12.8152 12.8152 34)
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# select particles in one side of the elongated box
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region left plane 0 0 10 0 0 1
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group left region left
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2688 atoms in group left
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velocity left create 6.0 1 mom yes rot yes
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# simulation parameters
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neighbor 0.6 bin
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timestep 0.004
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run_style verlet
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fix ensemble left nve # Note: only move particle in left-hand side
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fix langevin left langevin 3.0 0.8 100.0 2017
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# outout
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thermo_style custom step temp pzz pe lz
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thermo 100
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# dump dumpXYZ all xyz 100 traj.xyz
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# run reduced for demonstration purposes
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# run 10000
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run 5000
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.1
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ghost atom cutoff = 3.1
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binsize = 1.55, bins = 9 9 22
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes
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Step Temp Pzz PotEng Lz
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0 3.1494433 -3.4735106 -6.8707307 34
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100 1.7727555 6.5330255 -4.8035477 34
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200 1.7462368 7.0070325 -4.7646426 34
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300 1.7564888 6.6190123 -4.7894637 34
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400 1.7641186 6.609684 -4.8064772 34
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500 1.7383511 6.7304936 -4.7708095 34
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600 1.731708 6.8574656 -4.7612918 34
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700 1.7332167 6.6530919 -4.7670014 34
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800 1.7487537 6.5644963 -4.7907458 34
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900 1.7353648 6.7115188 -4.7772149 34
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1000 1.728878 6.4175719 -4.7797216 34
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1100 1.7471488 6.5346083 -4.813376 34
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1200 1.7188149 6.2502104 -4.7822235 34
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1300 1.7151194 6.792534 -4.7781701 34
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1400 1.7406603 6.6639592 -4.8170174 34
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1500 1.7090537 6.4677579 -4.770701 34
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1600 1.7014954 6.2853535 -4.7679742 34
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1700 1.7064354 6.4352857 -4.7812978 34
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1800 1.7169971 6.5808758 -4.799426 34
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1900 1.6822712 6.3746758 -4.7522464 34
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2000 1.7126546 6.534969 -4.8091595 34
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2100 1.7086108 6.4679932 -4.8146664 34
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2200 1.6974952 6.3802129 -4.8052505 34
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2300 1.6868035 6.4009243 -4.7935769 34
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2400 1.7107125 6.2318869 -4.8358765 34
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2500 1.660241 6.4891487 -4.7661183 34
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2600 1.6801816 6.1988356 -4.8024291 34
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2700 1.6940298 6.1328187 -4.8290053 34
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2800 1.6755061 6.4150693 -4.8145473 34
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2900 1.6749928 6.4248792 -4.8213509 34
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3000 1.6310737 6.6491291 -4.7673027 34
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3100 1.6559915 6.2726719 -4.8109181 34
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3200 1.6574579 5.7132029 -4.8189484 34
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3300 1.6816136 5.7697439 -4.8652811 34
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3400 1.6489483 6.4463349 -4.8247812 34
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3500 1.6557974 5.9763333 -4.8383712 34
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3600 1.6215459 6.2806534 -4.7954657 34
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3700 1.6484987 6.0671609 -4.8470777 34
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3800 1.6473922 5.8688108 -4.8555351 34
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3900 1.6435957 5.930425 -4.8562076 34
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4000 1.6514434 6.1962122 -4.872998 34
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4100 1.6138337 6.4808124 -4.8219373 34
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4200 1.6215239 5.9467966 -4.8412146 34
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4300 1.6129295 5.9377323 -4.8414596 34
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4400 1.6020549 6.1104301 -4.8395939 34
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4500 1.6047738 6.0816222 -4.8538151 34
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4600 1.6053565 6.183466 -4.8686817 34
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4700 1.6088152 5.7416542 -4.894114 34
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4800 1.5954309 5.694319 -4.8840198 34
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4900 1.5582564 6.1199614 -4.8429998 34
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5000 1.5786672 5.8813574 -4.8907344 34
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Loop time of 28.3867 on 1 procs for 5000 steps with 5120 atoms
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Performance: 60873.483 tau/day, 176.139 timesteps/s
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99.4% 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 | 22.269 | 22.269 | 22.269 | 0.0 | 78.45
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Neigh | 4.7222 | 4.7222 | 4.7222 | 0.0 | 16.64
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Comm | 0.40821 | 0.40821 | 0.40821 | 0.0 | 1.44
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Output | 0.0042329 | 0.0042329 | 0.0042329 | 0.0 | 0.01
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Modify | 0.88231 | 0.88231 | 0.88231 | 0.0 | 3.11
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Other | | 0.1005 | | | 0.35
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Nlocal: 5120 ave 5120 max 5120 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 7768 ave 7768 max 7768 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 297167 ave 297167 max 297167 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 297167
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Ave neighs/atom = 58.0404
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Neighbor list builds = 474
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Dangerous builds = 246
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write_data data.halfhalf
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Total wall time: 0:00:28
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