forked from lijiext/lammps
add example for using fix controller with a moving wall to adjust pressure
This commit is contained in:
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264dd59c75
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eeaeab0832
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt, thermostatted by fix controller
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units lj
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atom_style atomic
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boundary p p m
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processors * * 1
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 -4 14
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region slab block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 region slab
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Created 4200 atoms
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Time spent = 0.000752687 secs
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 2 every 2 check yes
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fix 1 all nve
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fix 3 all langevin 1.5 1.5 0.5 412513
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variable zhi internal $(10.5*zlat)
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variable zhi internal 17.635760009516324942
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variable kwall equal 20.0
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fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
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fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
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fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5
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variable pzz equal pzz
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fix ave all ave/time 10 10 100 v_pzz
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# equilibrate
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thermo_style custom step temp pxx pyy pzz f_ave v_zhi
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thermo 500
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run 2500
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Neighbor list info ...
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update every 2 steps, delay 2 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 = 12 12 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) = 3.639 | 3.639 | 3.639 Mbytes
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Step Temp Pxx Pyy Pzz f_ave v_zhi
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0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576
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500 1.4850596 3.1161377 2.9246345 2.9122136 2.9795403 17.63576
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1000 1.4706875 2.4918963 2.4698964 2.3538419 2.5181301 17.63576
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1500 1.4978967 1.9196563 2.0442863 1.978316 1.9215971 17.63576
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2000 1.4738152 1.6424128 1.5875245 1.7098788 1.6222172 17.63576
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2500 1.5012535 1.3324666 1.3078613 1.30772 1.3830807 17.63576
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Loop time of 9.88972 on 1 procs for 2500 steps with 4200 atoms
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Performance: 109204.308 tau/day, 252.788 timesteps/s
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99.8% 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 | 5.9583 | 5.9583 | 5.9583 | 0.0 | 60.25
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Neigh | 3.0444 | 3.0444 | 3.0444 | 0.0 | 30.78
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Comm | 0.095146 | 0.095146 | 0.095146 | 0.0 | 0.96
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Output | 0.00018764 | 0.00018764 | 0.00018764 | 0.0 | 0.00
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Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 7.45
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Other | | 0.05447 | | | 0.55
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Nlocal: 4200 ave 4200 max 4200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3278 ave 3278 max 3278 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 125488 ave 125488 max 125488 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 125488
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Ave neighs/atom = 29.8781
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Neighbor list builds = 414
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Dangerous builds = 0
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# use time averaged pressure for control
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#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi
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# use instantaneous pressure for control
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fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi
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# run with controller
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run 5000
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Per MPI rank memory allocation (min/avg/max) = 3.645 | 3.645 | 3.645 Mbytes
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Step Temp Pxx Pyy Pzz f_ave v_zhi
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2500 1.5012535 1.332723 1.3081129 1.3079716 1.3830807 17.63576
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3000 1.4976659 1.2148748 1.2873541 1.4929784 1.337029 17.052206
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3500 1.5099561 1.2602054 1.2429245 1.3566909 1.2922544 15.926241
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4000 1.4993048 1.3600782 1.2700229 1.441161 1.3958688 15.38517
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4500 1.5361306 1.4939463 1.4981484 1.6511208 1.4778535 15.14012
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5000 1.4858931 1.3755603 1.4202936 1.3321859 1.4463033 14.710626
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5500 1.495093 1.5412773 1.3726815 1.3337702 1.4661477 14.551062
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6000 1.4867063 1.4204076 1.4972286 1.5325972 1.5125403 14.727292
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6500 1.5036424 1.4449136 1.5290335 1.5163832 1.4974 14.866821
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7000 1.5376638 1.4409843 1.4434687 1.3927467 1.5097986 14.730925
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7500 1.4880255 1.4006281 1.4538957 1.4700911 1.4904586 14.531748
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Loop time of 18.1541 on 1 procs for 5000 steps with 4200 atoms
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Performance: 118981.600 tau/day, 275.420 timesteps/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 | 10.685 | 10.685 | 10.685 | 0.0 | 58.86
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Neigh | 5.6863 | 5.6863 | 5.6863 | 0.0 | 31.32
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Comm | 0.19485 | 0.19485 | 0.19485 | 0.0 | 1.07
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Output | 0.0003798 | 0.0003798 | 0.0003798 | 0.0 | 0.00
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Modify | 1.479 | 1.479 | 1.479 | 0.0 | 8.15
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Other | | 0.1086 | | | 0.60
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Nlocal: 4200 ave 4200 max 4200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3252 ave 3252 max 3252 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 126902 ave 126902 max 126902 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 126902
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Ave neighs/atom = 30.2148
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Neighbor list builds = 815
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Dangerous builds = 0
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Total wall time: 0:00:28
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@ -0,0 +1,142 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt, thermostatted by fix controller
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units lj
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atom_style atomic
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boundary p p m
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processors * * 1
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 -4 14
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region slab block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143)
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2 by 1 by 1 MPI processor grid
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create_atoms 1 region slab
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Created 4200 atoms
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Time spent = 0.00055027 secs
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 2 every 2 check yes
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fix 1 all nve
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fix 3 all langevin 1.5 1.5 0.5 412513
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variable zhi internal $(10.5*zlat)
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variable zhi internal 17.635760009516324942
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variable kwall equal 20.0
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fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
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fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5
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fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5
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variable pzz equal pzz
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fix ave all ave/time 10 10 100 v_pzz
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# equilibrate
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thermo_style custom step temp pxx pyy pzz f_ave v_zhi
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thermo 500
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run 2500
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Neighbor list info ...
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update every 2 steps, delay 2 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 = 12 12 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) = 3.205 | 3.205 | 3.205 Mbytes
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Step Temp Pxx Pyy Pzz f_ave v_zhi
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0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576
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500 1.4685077 2.9959993 2.9101136 2.9557017 2.9691654 17.63576
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1000 1.4660014 2.3677693 2.4832805 2.3853443 2.495998 17.63576
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1500 1.503875 1.9958194 1.8192177 1.8732779 1.9196618 17.63576
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2000 1.508944 1.6772869 1.6171356 1.5363361 1.6221247 17.63576
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2500 1.4754205 1.4808824 1.3803411 1.3538329 1.433588 17.63576
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Loop time of 5.20209 on 2 procs for 2500 steps with 4200 atoms
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Performance: 207608.821 tau/day, 480.576 timesteps/s
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99.2% CPU use with 2 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 | 3.0816 | 3.1008 | 3.1199 | 1.1 | 59.61
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Neigh | 1.5272 | 1.5364 | 1.5455 | 0.7 | 29.53
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Comm | 0.12968 | 0.15815 | 0.18662 | 7.2 | 3.04
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Output | 0.00012827 | 0.00048637 | 0.00084448 | 0.0 | 0.01
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Modify | 0.3743 | 0.37516 | 0.37602 | 0.1 | 7.21
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Other | | 0.03114 | | | 0.60
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Nlocal: 2100 ave 2121 max 2079 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 2593 ave 2606 max 2580 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 62766.5 ave 63603 max 61930 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 125533
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Ave neighs/atom = 29.8888
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Neighbor list builds = 410
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Dangerous builds = 0
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# use time averaged pressure for control
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#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi
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# use instantaneous pressure for control
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fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi
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# run with controller
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run 5000
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Per MPI rank memory allocation (min/avg/max) = 3.208 | 3.208 | 3.208 Mbytes
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Step Temp Pxx Pyy Pzz f_ave v_zhi
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2500 1.4754205 1.482216 1.3815843 1.3550522 1.433588 17.63576
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3000 1.4805196 1.4121967 1.3859531 1.4360385 1.3724589 16.755204
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3500 1.4909046 1.3658062 1.3441219 1.3839841 1.3998033 15.699356
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4000 1.500835 1.4985308 1.4043943 1.3989491 1.4418757 15.030304
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4500 1.5371526 1.4614358 1.4941526 1.455191 1.5121676 14.738878
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5000 1.4766657 1.4037866 1.2404757 1.3679074 1.4173969 14.670117
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5500 1.48302 1.5591058 1.3928461 1.3952178 1.5334476 14.58675
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6000 1.5191325 1.4416274 1.5290468 1.5077685 1.5176605 14.560389
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6500 1.495773 1.6695592 1.6621934 1.6073908 1.5508856 14.668722
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7000 1.5033866 1.48723 1.5054815 1.4755225 1.5024653 14.676533
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7500 1.5512429 1.6282941 1.7399228 1.6351273 1.6851571 14.671092
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Loop time of 9.76074 on 2 procs for 5000 steps with 4200 atoms
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Performance: 221294.755 tau/day, 512.256 timesteps/s
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98.5% CPU use with 2 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 | 5.5979 | 5.6281 | 5.6583 | 1.3 | 57.66
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Neigh | 2.9053 | 2.9335 | 2.9618 | 1.6 | 30.05
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Comm | 0.31645 | 0.37703 | 0.43762 | 9.9 | 3.86
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Output | 0.00025439 | 0.0009656 | 0.0016768 | 0.0 | 0.01
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Modify | 0.75674 | 0.75966 | 0.76258 | 0.3 | 7.78
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Other | | 0.06145 | | | 0.63
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Nlocal: 2100 ave 2109 max 2091 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 2578 ave 2578 max 2578 min
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Histogram: 2 0 0 0 0 0 0 0 0 0
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Neighs: 63578.5 ave 64145 max 63012 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 127157
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Ave neighs/atom = 30.2755
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Neighbor list builds = 816
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Dangerous builds = 0
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Total wall time: 0:00:14
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