added an example for recalculating the RDF at a longer cutoff via rerun
This commit is contained in:
Steve Plimpton
17
examples/rerun/README
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17
examples/rerun/README
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Examples of how to use the rerun and read_dump commands
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in.first - run on any number of procs for any size problem
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in.rerun - run on same or different proc count for same size problem
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in.read_dump - ditto to in.rerun
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The thermo output on the same timesteps should be identical
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to within round-off errors.
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in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma
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in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma
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In both bases the time averaged RDF is computed 10x times, every 100
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steps for 1000 total. In the rerun, the pair style cutoff is changed
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so the RDF can be computed to a longer distance without re-running the
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simulation. The RDF values in the 2 files should be the same (within
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round-off) for the first 50 bins.
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36
examples/rerun/in.rdf.first
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36
examples/rerun/in.rdf.first
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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 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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dump 1 all custom 100 lj.dump id type x y z
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compute myRDF all rdf 50 cutoff 2.5
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fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
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thermo 100
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run 1000
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31
examples/rerun/in.rdf.rerun
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31
examples/rerun/in.rdf.rerun
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$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 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style lj/cut 5.0
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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compute myRDF all rdf 100 cutoff 5.0
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fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
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thermo 100
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rerun lj.dump dump x y z
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105
examples/rerun/log.20Jan20.rdf.first.g++.4
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105
examples/rerun/log.20Jan20.rdf.first.g++.4
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LAMMPS (09 Jan 2020)
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$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 = 0.00100017 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
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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
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compute myRDF all rdf 50 cutoff 2.5
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fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
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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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2 neighbor lists, perpetual/occasional/extra = 1 1 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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(2) compute rdf, occasional
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attributes: half, newton on, cut 2.8
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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) = 8.487 | 8.487 | 8.487 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 7.44016 on 4 procs for 1000 steps with 32000 atoms
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Performance: 58063.267 tau/day, 134.406 timesteps/s
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99.7% 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 | 5.3881 | 5.5809 | 5.7111 | 5.4 | 75.01
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Neigh | 0.80101 | 0.82776 | 0.85702 | 2.2 | 11.13
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Comm | 0.31801 | 0.48426 | 0.72201 | 22.5 | 6.51
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Output | 0.17801 | 0.17801 | 0.17801 | 0.0 | 2.39
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Modify | 0.31201 | 0.33076 | 0.33701 | 1.9 | 4.45
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Other | | 0.0385 | | | 0.52
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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: 0:00:07
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100
examples/rerun/log.20Jan20.rdf.rerun.g++.4
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100
examples/rerun/log.20Jan20.rdf.rerun.g++.4
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@ -0,0 +1,100 @@
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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 = 0.00183487 secs
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mass 1 1.0
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pair_style lj/cut 5.0
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pair_coeff 1 1 1.0 1.0
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neighbor 0.3 bin
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compute myRDF all rdf 100 cutoff 5.0
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fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
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thermo 100
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rerun lj.dump dump x y z
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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 = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 13 13 13
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2 neighbor lists, perpetual/occasional/extra = 1 1 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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(2) compute rdf, occasional
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attributes: half, newton on, cut 5.3
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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) = 15.19 | 15.19 | 15.19 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -7.1616928 0 -7.1616928 -6.8899898
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100 0 -6.1442754 0 -6.1442754 -1.0825318
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200 0 -6.1472483 0 -6.1472483 -1.0817213
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300 0 -6.1274033 0 -6.1274033 -0.95961014
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400 0 -6.1202956 0 -6.1202956 -0.8988851
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500 0 -6.1067136 0 -6.1067136 -0.82660368
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600 0 -6.0893179 0 -6.0893179 -0.70264528
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700 0 -6.0803044 0 -6.0803044 -0.64232743
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800 0 -6.0710303 0 -6.0710303 -0.5824798
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900 0 -6.0698963 0 -6.0698963 -0.58057929
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1000 0 -6.0627642 0 -6.0627642 -0.53599799
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Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms
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Performance: 1544.558 tau/day, 3.575 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 | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 3.077 | | |100.00
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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: 20028 ave 20060 max 19988 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Total # of neighbors = 8416685
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Ave neighs/atom = 263.021
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:03
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54
examples/rerun/rdf.20Jan20.first.g++.4
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54
examples/rerun/rdf.20Jan20.first.g++.4
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@ -0,0 +1,54 @@
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# Time-averaged data for fix 2
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# TimeStep Number-of-rows
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# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
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1000 50
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1 0.025 0 0
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2 0.075 0 0
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3 0.125 0 0
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4 0.175 0 0
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5 0.225 0 0
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6 0.275 0 0
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7 0.325 0 0
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8 0.375 0 0
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9 0.425 0 0
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10 0.475 0 0
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11 0.525 0 0
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12 0.575 0 0
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13 0.625 0 0
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14 0.675 0 0
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15 0.725 0 0
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16 0.775 0 0
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17 0.825 0 0
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18 0.875 1.53863e-05 6.25e-06
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19 0.925 0.0217263 0.00986875
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20 0.975 0.506735 0.265431
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21 1.025 1.92083 1.33605
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22 1.075 2.8749 3.09855
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23 1.125 2.7805 4.96541
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24 1.175 2.21879 6.59047
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25 1.225 1.67622 7.92484
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26 1.275 1.25407 9.00629
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27 1.325 0.963413 9.90353
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28 1.375 0.774441 10.6802
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29 1.425 0.656196 11.3871
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30 1.475 0.589364 12.0672
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31 1.525 0.560681 12.7589
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32 1.575 0.560195 13.4961
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33 1.625 0.587995 14.3197
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34 1.675 0.632155 15.2605
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35 1.725 0.706585 16.3758
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36 1.775 0.805303 17.7216
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37 1.825 0.925415 19.3565
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38 1.875 1.05672 21.3271
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39 1.925 1.17634 23.6394
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40 1.975 1.2557 26.2375
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41 2.025 1.30009 29.0653
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42 2.075 1.30889 32.0546
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43 2.125 1.27704 35.1135
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44 2.175 1.21808 38.17
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45 2.225 1.13622 41.1536
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46 2.275 1.05072 44.0382
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47 2.325 0.973786 46.8303
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48 2.375 0.910095 49.5533
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49 2.425 0.866474 52.256
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50 2.475 0.841724 54.991
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104
examples/rerun/rdf.20Jan20.rerun.g++.4
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104
examples/rerun/rdf.20Jan20.rerun.g++.4
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@ -0,0 +1,104 @@
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# Time-averaged data for fix 2
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# TimeStep Number-of-rows
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# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
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1000 100
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1 0.025 0 0
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2 0.075 0 0
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3 0.125 0 0
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4 0.175 0 0
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5 0.225 0 0
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6 0.275 0 0
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||||
7 0.325 0 0
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8 0.375 0 0
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||||
9 0.425 0 0
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||||
10 0.475 0 0
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||||
11 0.525 0 0
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12 0.575 0 0
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||||
13 0.625 0 0
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14 0.675 0 0
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15 0.725 0 0
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||||
16 0.775 0 0
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||||
17 0.825 0 0
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||||
18 0.875 1.53863e-05 6.25e-06
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19 0.925 0.021685 0.00985
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20 0.975 0.506834 0.265463
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21 1.025 1.92047 1.33588
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||||
22 1.075 2.87514 3.09853
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||||
23 1.125 2.78062 4.96547
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||||
24 1.175 2.21869 6.59046
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||||
25 1.225 1.67626 7.92486
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||||
26 1.275 1.25409 9.00633
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||||
27 1.325 0.963245 9.90341
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||||
28 1.375 0.774535 10.6802
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||||
29 1.425 0.65626 11.3871
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||||
30 1.475 0.58925 12.0672
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||||
31 1.525 0.560782 12.759
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32 1.575 0.560133 13.496
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33 1.625 0.588008 14.3197
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34 1.675 0.632185 15.2605
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35 1.725 0.706541 16.3757
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36 1.775 0.805341 17.7216
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37 1.825 0.925351 19.3565
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||||
38 1.875 1.05677 21.3271
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39 1.925 1.17639 23.6395
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40 1.975 1.25571 26.2376
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41 2.025 1.30011 29.0655
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||||
42 2.075 1.30883 32.0547
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43 2.125 1.27702 35.1134
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44 2.175 1.21813 38.17
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45 2.225 1.13617 41.1536
|
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46 2.275 1.05073 44.0382
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47 2.325 0.97376 46.8302
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48 2.375 0.91012 49.5533
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||||
49 2.425 0.866556 52.2563
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||||
50 2.475 0.841651 54.991
|
||||
51 2.525 0.839516 57.8301
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52 2.575 0.848795 60.8153
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53 2.625 0.868861 63.991
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||||
54 2.675 0.896335 67.393
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||||
55 2.725 0.925794 71.0395
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||||
56 2.775 0.961909 74.9685
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||||
57 2.825 0.999727 79.2005
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||||
58 2.875 1.03745 83.749
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||||
59 2.925 1.07355 88.6208
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60 2.975 1.10406 93.8039
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||||
61 3.025 1.11993 99.2397
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||||
62 3.075 1.12062 104.86
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||||
63 3.125 1.10531 110.586
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||||
64 3.175 1.07711 116.345
|
||||
65 3.225 1.04268 122.097
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||||
66 3.275 1.00838 127.834
|
||||
67 3.325 0.974855 133.55
|
||||
68 3.375 0.949817 139.289
|
||||
69 3.425 0.936519 145.116
|
||||
70 3.475 0.92942 151.069
|
||||
71 3.525 0.930926 157.205
|
||||
72 3.575 0.940561 163.581
|
||||
73 3.625 0.94956 170.199
|
||||
74 3.675 0.964202 177.107
|
||||
75 3.725 0.97905 184.312
|
||||
76 3.775 0.991906 191.81
|
||||
77 3.825 1.00093 199.577
|
||||
78 3.875 1.01248 207.641
|
||||
79 3.925 1.02301 216.001
|
||||
80 3.975 1.03474 224.673
|
||||
81 4.025 1.04171 233.624
|
||||
82 4.075 1.04725 242.849
|
||||
83 4.125 1.04997 252.325
|
||||
84 4.175 1.04758 262.01
|
||||
85 4.225 1.03985 271.856
|
||||
86 4.275 1.02755 281.817
|
||||
87 4.325 1.00883 291.826
|
||||
88 4.375 0.99045 301.882
|
||||
89 4.425 0.97287 311.986
|
||||
90 4.475 0.958469 322.166
|
||||
91 4.525 0.952552 332.512
|
||||
92 4.575 0.948064 343.037
|
||||
93 4.625 0.952592 353.845
|
||||
94 4.675 0.958837 364.96
|
||||
95 4.725 0.970831 376.457
|
||||
96 4.775 0.985248 388.372
|
||||
97 4.825 0.998873 400.707
|
||||
98 4.875 1.0119 413.462
|
||||
99 4.925 1.02446 426.643
|
||||
100 4.975 1.03613 440.245
|
||||
Reference in New Issue
Block a user