added rerun example dir
This commit is contained in:
Steve Plimpton
@ -101,6 +101,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si
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python: use of PYTHON package to invoke Python code from input script
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python: use of PYTHON package to invoke Python code from input script
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qeq: use of QEQ package for charge equilibration
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qeq: use of QEQ package for charge equilibration
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reax: RDX and TATB and several other models using ReaxFF
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reax: RDX and TATB and several other models using ReaxFF
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rerun: use of rerun and read_dump commands
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rigid: rigid bodies modeled as independent or coupled
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void
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shear: sideways shear applied to 2d solid, with and without a void
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snap: examples for using several bundled SNAP potentials
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snap: examples for using several bundled SNAP potentials
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33
examples/rerun/in.first
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33
examples/rerun/in.first
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@ -0,0 +1,33 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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dump 1 all custom 100 lj.dump id type x y z vx vy vz
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thermo 100
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run 1000
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37
examples/rerun/in.read_dump
Normal file
37
examples/rerun/in.read_dump
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@ -0,0 +1,37 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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thermo 100
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read_dump lj.dump 200 x y z vx vy vz
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run 0 post no
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read_dump lj.dump 800 x y z vx vy vz
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run 0 post no
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read_dump lj.dump 600 x y z vx vy vz
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run 0 post no
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read_dump lj.dump 400 x y z vx vy vz
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run 0 post no
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29
examples/rerun/in.rerun
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29
examples/rerun/in.rerun
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@ -0,0 +1,29 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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thermo 100
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rerun lj.dump first 200 last 800 every 200 &
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dump x y z vx vy vz
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97
examples/rerun/log.20Jan20.first.g++.4
Normal file
97
examples/rerun/log.20Jan20.first.g++.4
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@ -0,0 +1,97 @@
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LAMMPS (09 Jan 2020)
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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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 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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create_atoms CPU = 0.00173283 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 0 every 20 check no
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fix 1 all nve
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dump 1 all custom 100 lj.dump id type x y z vx vy vz
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thermo 100
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run 1000
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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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 = 24 24 24
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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) = 7.869 | 7.869 | 7.869 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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200 0.75953175 -5.7618892 0 -4.6226272 0.20910575
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300 0.74624286 -5.741962 0 -4.6226327 0.32016436
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400 0.74155675 -5.7343359 0 -4.6220356 0.3777989
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500 0.73249345 -5.7206946 0 -4.6219887 0.44253023
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600 0.72087255 -5.7029314 0 -4.6216563 0.55730354
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700 0.71489947 -5.693532 0 -4.6212164 0.61322381
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800 0.70876958 -5.6840594 0 -4.6209382 0.66822293
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900 0.70799522 -5.6828388 0 -4.6208791 0.66961272
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1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575
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Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms
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Performance: 68193.673 tau/day, 157.856 timesteps/s
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99.8% CPU use with 4 MPI tasks x no 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 | 4.3538 | 4.6712 | 5.0021 | 12.8 | 73.74
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Neigh | 0.59378 | 0.65229 | 0.75202 | 8.0 | 10.30
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Comm | 0.28101 | 0.69839 | 1.0586 | 38.5 | 11.02
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Output | 0.21601 | 0.21682 | 0.21718 | 0.1 | 3.42
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Modify | 0.074002 | 0.074803 | 0.075779 | 0.2 | 1.18
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Other | | 0.0214 | | | 0.34
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Nlocal: 8000 ave 8049 max 7942 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Nghost: 8632.5 ave 8685 max 8591 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Neighs: 299934 ave 303105 max 295137 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 1199738
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Ave neighs/atom = 37.4918
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:06
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118
examples/rerun/log.20Jan20.read_dump.g++.4
Normal file
118
examples/rerun/log.20Jan20.read_dump.g++.4
Normal file
@ -0,0 +1,118 @@
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LAMMPS (09 Jan 2020)
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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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 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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create_atoms CPU = 0.001724 secs
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mass 1 1.0
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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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thermo 100
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read_dump lj.dump 200 x y z vx vy vz
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orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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32000 atoms before read
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32000 atoms in snapshot
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0 atoms purged
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32000 atoms replaced
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0 atoms trimmed
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0 atoms added
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32000 atoms after read
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run 0 post no
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 24 24 24
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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) = 6.841 | 6.843 | 6.846 Mbytes
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Step Temp E_pair E_mol TotEng Press
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200 0.75953173 -5.7618854 0 -4.6226234 0.20912952
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Loop time of 2.26498e-06 on 4 procs for 0 steps with 32000 atoms
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read_dump lj.dump 800 x y z vx vy vz
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orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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32000 atoms before read
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32000 atoms in snapshot
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0 atoms purged
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32000 atoms replaced
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0 atoms trimmed
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0 atoms added
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32000 atoms after read
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run 0 post no
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
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Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
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Step Temp E_pair E_mol TotEng Press
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800 0.70876957 -5.6840545 0 -4.6209334 0.66823926
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Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
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read_dump lj.dump 600 x y z vx vy vz
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orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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32000 atoms before read
|
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32000 atoms in snapshot
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0 atoms purged
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||||||
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32000 atoms replaced
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||||||
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0 atoms trimmed
|
||||||
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0 atoms added
|
||||||
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32000 atoms after read
|
||||||
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run 0 post no
|
||||||
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
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Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
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Step Temp E_pair E_mol TotEng Press
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600 0.72087256 -5.7029306 0 -4.6216556 0.55729873
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Loop time of 7.7486e-07 on 4 procs for 0 steps with 32000 atoms
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read_dump lj.dump 400 x y z vx vy vz
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orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
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||||||
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32000 atoms before read
|
||||||
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32000 atoms in snapshot
|
||||||
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0 atoms purged
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||||||
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32000 atoms replaced
|
||||||
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0 atoms trimmed
|
||||||
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0 atoms added
|
||||||
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32000 atoms after read
|
||||||
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run 0 post no
|
||||||
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
||||||
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Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
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||||||
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Step Temp E_pair E_mol TotEng Press
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||||||
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400 0.74155677 -5.7343336 0 -4.6220332 0.37780193
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||||||
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Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
|
||||||
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|
||||||
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Total wall time: 0:00:00
|
||||||
86
examples/rerun/log.20Jan20.rerun.g++.4
Normal file
86
examples/rerun/log.20Jan20.rerun.g++.4
Normal file
@ -0,0 +1,86 @@
|
|||||||
|
LAMMPS (09 Jan 2020)
|
||||||
|
# 3d Lennard-Jones melt
|
||||||
|
|
||||||
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variable x index 1
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||||||
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variable y index 1
|
||||||
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variable z index 1
|
||||||
|
|
||||||
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variable xx equal 20*$x
|
||||||
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variable xx equal 20*1
|
||||||
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variable yy equal 20*$y
|
||||||
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variable yy equal 20*1
|
||||||
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variable zz equal 20*$z
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||||||
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variable zz equal 20*1
|
||||||
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|
||||||
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units lj
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||||||
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atom_style atomic
|
||||||
|
|
||||||
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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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||||||
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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||||||
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region box block 0 20 0 ${yy} 0 ${zz}
|
||||||
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region box block 0 20 0 20 0 ${zz}
|
||||||
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region box block 0 20 0 20 0 20
|
||||||
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create_box 1 box
|
||||||
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Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||||
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1 by 2 by 2 MPI processor grid
|
||||||
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create_atoms 1 box
|
||||||
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Created 32000 atoms
|
||||||
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create_atoms CPU = 0.00100017 secs
|
||||||
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mass 1 1.0
|
||||||
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|
||||||
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pair_style lj/cut 2.5
|
||||||
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pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
rerun lj.dump first 200 last 800 every 200 dump x y z vx vy vz
|
||||||
|
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 24 24 24
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.716 | 6.718 | 6.721 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
200 0.75953173 -5.7618854 0 -4.6226234 0.20912952
|
||||||
|
400 0.74155677 -5.7343336 0 -4.6220332 0.37780193
|
||||||
|
600 0.72087256 -5.7029306 0 -4.6216556 0.55729873
|
||||||
|
800 0.70876957 -5.6840545 0 -4.6209334 0.66823926
|
||||||
|
Loop time of 0.375898 on 4 procs for 4 steps with 32000 atoms
|
||||||
|
|
||||||
|
Performance: 4596.990 tau/day, 10.641 timesteps/s
|
||||||
|
98.0% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.3759 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 8000 ave 8073 max 7933 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
Nghost: 8693.25 ave 8731 max 8658 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 299786 ave 302947 max 293888 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1199142
|
||||||
|
Ave neighs/atom = 37.4732
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user