Loading examples/rerun/README 0 → 100644 +17 −0 Original line number Diff line number Diff line Examples of how to use the rerun and read_dump commands in.first - run on any number of procs for any size problem in.rerun - run on same or different proc count for same size problem in.read_dump - ditto to in.rerun The thermo output on the same timesteps should be identical to within round-off errors. in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma In both bases the time averaged RDF is computed 10x times, every 100 steps for 1000 total. In the rerun, the pair style cutoff is changed so the RDF can be computed to a longer distance without re-running the simulation. The RDF values in the 2 files should be the same (within round-off) for the first 50 bins. examples/rerun/in.rdf.first 0 → 100644 +36 −0 Original line number Diff line number Diff line # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z units lj atom_style atomic lattice fcc 0.8442 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve dump 1 all custom 100 lj.dump id type x y z compute myRDF all rdf 50 cutoff 2.5 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector thermo 100 run 1000 examples/rerun/in.rdf.rerun 0 → 100644 +31 −0 Original line number Diff line number Diff line # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z units lj atom_style atomic lattice fcc 0.8442 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box mass 1 1.0 pair_style lj/cut 5.0 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin compute myRDF all rdf 100 cutoff 5.0 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector thermo 100 rerun lj.dump dump x y z examples/rerun/log.20Jan20.rdf.first.g++.4 0 → 100644 +105 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.00100017 secs mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve dump 1 all custom 100 lj.dump id type x y z compute myRDF all rdf 50 cutoff 2.5 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector thermo 100 run 1000 Neighbor list info ... update every 20 steps, delay 0 steps, check no 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 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) compute rdf, occasional attributes: half, newton on, cut 2.8 pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 200 0.75953175 -5.7618892 0 -4.6226272 0.20910575 300 0.74624286 -5.741962 0 -4.6226327 0.32016436 400 0.74155675 -5.7343359 0 -4.6220356 0.3777989 500 0.73249345 -5.7206946 0 -4.6219887 0.44253023 600 0.72087255 -5.7029314 0 -4.6216563 0.55730354 700 0.71489947 -5.693532 0 -4.6212164 0.61322381 800 0.70876958 -5.6840594 0 -4.6209382 0.66822293 900 0.70799522 -5.6828388 0 -4.6208791 0.66961272 1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575 Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms Performance: 58063.267 tau/day, 134.406 timesteps/s 99.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3881 | 5.5809 | 5.7111 | 5.4 | 75.01 Neigh | 0.80101 | 0.82776 | 0.85702 | 2.2 | 11.13 Comm | 0.31801 | 0.48426 | 0.72201 | 22.5 | 6.51 Output | 0.17801 | 0.17801 | 0.17801 | 0.0 | 2.39 Modify | 0.31201 | 0.33076 | 0.33701 | 1.9 | 4.45 Other | | 0.0385 | | | 0.52 Nlocal: 8000 ave 8049 max 7942 min Histogram: 1 0 0 1 0 0 0 1 0 1 Nghost: 8632.5 ave 8685 max 8591 min Histogram: 1 0 0 1 1 0 0 0 0 1 Neighs: 299934 ave 303105 max 295137 min Histogram: 1 0 0 0 0 0 1 1 0 1 Total # of neighbors = 1199738 Ave neighs/atom = 37.4918 Neighbor list builds = 50 Dangerous builds not checked Total wall time: 0:00:07 examples/rerun/log.20Jan20.rdf.rerun.g++.4 0 → 100644 +100 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.00183487 secs mass 1 1.0 pair_style lj/cut 5.0 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin compute myRDF all rdf 100 cutoff 5.0 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector thermo 100 rerun lj.dump dump x y z Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65, bins = 13 13 13 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) compute rdf, occasional attributes: half, newton on, cut 5.3 pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7.1616928 0 -7.1616928 -6.8899898 100 0 -6.1442754 0 -6.1442754 -1.0825318 200 0 -6.1472483 0 -6.1472483 -1.0817213 300 0 -6.1274033 0 -6.1274033 -0.95961014 400 0 -6.1202956 0 -6.1202956 -0.8988851 500 0 -6.1067136 0 -6.1067136 -0.82660368 600 0 -6.0893179 0 -6.0893179 -0.70264528 700 0 -6.0803044 0 -6.0803044 -0.64232743 800 0 -6.0710303 0 -6.0710303 -0.5824798 900 0 -6.0698963 0 -6.0698963 -0.58057929 1000 0 -6.0627642 0 -6.0627642 -0.53599799 Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms Performance: 1544.558 tau/day, 3.575 timesteps/s 99.8% 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 | | 3.077 | | |100.00 Nlocal: 8000 ave 8049 max 7942 min Histogram: 1 0 0 1 0 0 0 1 0 1 Nghost: 20028 ave 20060 max 19988 min Histogram: 1 0 0 0 1 0 0 0 1 1 Neighs: 2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min Histogram: 1 0 0 1 0 0 0 0 1 1 Total # of neighbors = 8416685 Ave neighs/atom = 263.021 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:03 Loading
examples/rerun/README 0 → 100644 +17 −0 Original line number Diff line number Diff line Examples of how to use the rerun and read_dump commands in.first - run on any number of procs for any size problem in.rerun - run on same or different proc count for same size problem in.read_dump - ditto to in.rerun The thermo output on the same timesteps should be identical to within round-off errors. in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma In both bases the time averaged RDF is computed 10x times, every 100 steps for 1000 total. In the rerun, the pair style cutoff is changed so the RDF can be computed to a longer distance without re-running the simulation. The RDF values in the 2 files should be the same (within round-off) for the first 50 bins.
examples/rerun/in.rdf.first 0 → 100644 +36 −0 Original line number Diff line number Diff line # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z units lj atom_style atomic lattice fcc 0.8442 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve dump 1 all custom 100 lj.dump id type x y z compute myRDF all rdf 50 cutoff 2.5 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector thermo 100 run 1000
examples/rerun/in.rdf.rerun 0 → 100644 +31 −0 Original line number Diff line number Diff line # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z units lj atom_style atomic lattice fcc 0.8442 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box mass 1 1.0 pair_style lj/cut 5.0 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin compute myRDF all rdf 100 cutoff 5.0 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector thermo 100 rerun lj.dump dump x y z
examples/rerun/log.20Jan20.rdf.first.g++.4 0 → 100644 +105 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.00100017 secs mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve dump 1 all custom 100 lj.dump id type x y z compute myRDF all rdf 50 cutoff 2.5 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector thermo 100 run 1000 Neighbor list info ... update every 20 steps, delay 0 steps, check no 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 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) compute rdf, occasional attributes: half, newton on, cut 2.8 pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 200 0.75953175 -5.7618892 0 -4.6226272 0.20910575 300 0.74624286 -5.741962 0 -4.6226327 0.32016436 400 0.74155675 -5.7343359 0 -4.6220356 0.3777989 500 0.73249345 -5.7206946 0 -4.6219887 0.44253023 600 0.72087255 -5.7029314 0 -4.6216563 0.55730354 700 0.71489947 -5.693532 0 -4.6212164 0.61322381 800 0.70876958 -5.6840594 0 -4.6209382 0.66822293 900 0.70799522 -5.6828388 0 -4.6208791 0.66961272 1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575 Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms Performance: 58063.267 tau/day, 134.406 timesteps/s 99.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3881 | 5.5809 | 5.7111 | 5.4 | 75.01 Neigh | 0.80101 | 0.82776 | 0.85702 | 2.2 | 11.13 Comm | 0.31801 | 0.48426 | 0.72201 | 22.5 | 6.51 Output | 0.17801 | 0.17801 | 0.17801 | 0.0 | 2.39 Modify | 0.31201 | 0.33076 | 0.33701 | 1.9 | 4.45 Other | | 0.0385 | | | 0.52 Nlocal: 8000 ave 8049 max 7942 min Histogram: 1 0 0 1 0 0 0 1 0 1 Nghost: 8632.5 ave 8685 max 8591 min Histogram: 1 0 0 1 1 0 0 0 0 1 Neighs: 299934 ave 303105 max 295137 min Histogram: 1 0 0 0 0 0 1 1 0 1 Total # of neighbors = 1199738 Ave neighs/atom = 37.4918 Neighbor list builds = 50 Dangerous builds not checked Total wall time: 0:00:07
examples/rerun/log.20Jan20.rdf.rerun.g++.4 0 → 100644 +100 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.00183487 secs mass 1 1.0 pair_style lj/cut 5.0 pair_coeff 1 1 1.0 1.0 neighbor 0.3 bin compute myRDF all rdf 100 cutoff 5.0 fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector thermo 100 rerun lj.dump dump x y z Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65, bins = 13 13 13 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard (2) compute rdf, occasional attributes: half, newton on, cut 5.3 pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7.1616928 0 -7.1616928 -6.8899898 100 0 -6.1442754 0 -6.1442754 -1.0825318 200 0 -6.1472483 0 -6.1472483 -1.0817213 300 0 -6.1274033 0 -6.1274033 -0.95961014 400 0 -6.1202956 0 -6.1202956 -0.8988851 500 0 -6.1067136 0 -6.1067136 -0.82660368 600 0 -6.0893179 0 -6.0893179 -0.70264528 700 0 -6.0803044 0 -6.0803044 -0.64232743 800 0 -6.0710303 0 -6.0710303 -0.5824798 900 0 -6.0698963 0 -6.0698963 -0.58057929 1000 0 -6.0627642 0 -6.0627642 -0.53599799 Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms Performance: 1544.558 tau/day, 3.575 timesteps/s 99.8% 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 | | 3.077 | | |100.00 Nlocal: 8000 ave 8049 max 7942 min Histogram: 1 0 0 1 0 0 0 1 0 1 Nghost: 20028 ave 20060 max 19988 min Histogram: 1 0 0 0 1 0 0 0 1 1 Neighs: 2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min Histogram: 1 0 0 1 0 0 0 0 1 1 Total # of neighbors = 8416685 Ave neighs/atom = 263.021 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:03
