add new grid-based examples
This commit is contained in:
Steve Plimpton
@ -40,10 +40,22 @@ thermo 100
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thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
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thermo_modify format float "%20.16g"
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compute 10 all property/grid 10 10 10 id xc yc zc
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fix ave all ave/grid 100 5 500 10 10 10 f_twotemp:grid:data
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dump ave all grid 500 tmp.dump.ave &
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c_10:grid:data[*] f_ave:grid:data
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dump_modify ave sort 1
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# dump output
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#compute 1 all property/grid 10 10 10 id ix iy iz
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#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data
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#dump_modify 1 sort 1
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#compute 10 all property/grid 10 10 10 id xc yc zc
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#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data
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#dump ave all grid 100 tmp.dump.ave &
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# c_10:grid:data[*] f_ave:grid:data
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#dump_modify ave sort id
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#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data
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#dump_modify vtk sort id buffer no
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# run simulation
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run 1000
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@ -1,4 +1,4 @@
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LAMMPS (3 Aug 2022)
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LAMMPS (3 Nov 2022)
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units metal
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atom_style atomic
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boundary p p p
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@ -34,7 +34,7 @@ region atom_box block -10 10 -10 10 -10 10 units lattice
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create_atoms 1 region atom_box
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Created 16000 atoms
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using lattice units in orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7)
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create_atoms CPU = 0.004 seconds
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create_atoms CPU = 0.002 seconds
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mass 1 55.845
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@ -58,9 +58,22 @@ thermo 100
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thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
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thermo_modify format float "%20.16g"
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compute 10 all property/grid 10 10 10 id xc yc zc
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fix ave all ave/grid 100 5 500 10 10 10 f_twotemp:grid:data
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dump ave all grid 500 tmp.dump.ave c_10:grid:data[*] f_ave:grid:data
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# dump output
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#compute 1 all property/grid 10 10 10 id ix iy iz
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#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data
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#dump_modify 1 sort 1
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#compute 10 all property/grid 10 10 10 id xc yc zc
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#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data
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#dump ave all grid 100 tmp.dump.ave # c_10:grid:data[*] f_ave:grid:data
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#dump_modify ave sort id
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#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data
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#dump_modify vtk sort id buffer no
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# run simulation
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run 1000
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Neighbor list info ...
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@ -75,7 +88,7 @@ Neighbor list info ...
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.09 | 12.09 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 10.99 | 10.99 | 10.99 Mbytes
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Step Temp TotEng f_twotemp[1] f_twotemp[2]
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0 0 -68483.52254543516 371.9188105082105 0
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100 17.01353086098387 -68446.50228930202 334.6217068813629 0.3763710887774046
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@ -88,20 +101,20 @@ Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.09 | 12.09 Mbytes
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800 50.4375018189932 -68272.72651051797 160.995046695269 0.1708386295858845
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900 52.17011714635106 -68257.85059865142 146.1567281868867 0.1032829304640776
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1000 53.49296457217382 -68244.38715993936 132.7166474251702 0.06428993394665769
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Loop time of 15.6373 on 1 procs for 1000 steps with 16000 atoms
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Loop time of 5.99191 on 1 procs for 1000 steps with 16000 atoms
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Performance: 0.553 ns/day, 43.437 hours/ns, 63.950 timesteps/s
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Performance: 1.442 ns/day, 16.644 hours/ns, 166.892 timesteps/s, 2.670 Matom-step/s
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100.0% CPU use with 1 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 | 14.493 | 14.493 | 14.493 | 0.0 | 92.68
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Pair | 5.3136 | 5.3136 | 5.3136 | 0.0 | 88.68
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.088097 | 0.088097 | 0.088097 | 0.0 | 0.56
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Output | 0.0044447 | 0.0044447 | 0.0044447 | 0.0 | 0.03
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Modify | 1.0075 | 1.0075 | 1.0075 | 0.0 | 6.44
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Other | | 0.04433 | | | 0.28
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Comm | 0.035738 | 0.035738 | 0.035738 | 0.0 | 0.60
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Output | 0.00049119 | 0.00049119 | 0.00049119 | 0.0 | 0.01
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Modify | 0.62365 | 0.62365 | 0.62365 | 0.0 | 10.41
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Other | | 0.01844 | | | 0.31
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Nlocal: 16000 ave 16000 max 16000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -114,4 +127,4 @@ Total # of neighbors = 896000
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Ave neighs/atom = 56
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:15
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Total wall time: 0:00:06
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@ -1,5 +1,5 @@
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LAMMPS (3 Aug 2022)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:524)
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LAMMPS (3 Nov 2022)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
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units metal
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atom_style atomic
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boundary p p p
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@ -35,7 +35,7 @@ region atom_box block -10 10 -10 10 -10 10 units lattice
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create_atoms 1 region atom_box
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Created 16000 atoms
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using lattice units in orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7)
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create_atoms CPU = 0.002 seconds
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create_atoms CPU = 0.001 seconds
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mass 1 55.845
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@ -59,10 +59,22 @@ thermo 100
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thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
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thermo_modify format float "%20.16g"
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compute 10 all property/grid 10 10 10 id xc yc zc
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fix ave all ave/grid 100 5 500 10 10 10 f_twotemp:grid:data
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dump ave all grid 500 tmp.dump.ave c_10:grid:data[*] f_ave:grid:data
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dump_modify ave sort 1
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# dump output
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#compute 1 all property/grid 10 10 10 id ix iy iz
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#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data
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#dump_modify 1 sort 1
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#compute 10 all property/grid 10 10 10 id xc yc zc
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#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data
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#dump ave all grid 100 tmp.dump.ave # c_10:grid:data[*] f_ave:grid:data
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#dump_modify ave sort id
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#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data
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#dump_modify vtk sort id buffer no
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# run simulation
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run 1000
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Neighbor list info ...
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@ -77,7 +89,7 @@ Neighbor list info ...
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.903 | 5.904 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 4.843 | 4.843 | 4.843 Mbytes
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Step Temp TotEng f_twotemp[1] f_twotemp[2]
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0 0 -68483.52254530673 371.9188105082186 0
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100 16.95536995775684 -68446.64765713879 334.7745598327931 0.3602932995006087
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@ -90,20 +102,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.903 | 5.904 Mbytes
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800 49.66707856481075 -68274.98092841901 163.2540575286425 0.1600890300738265
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900 52.17692450487317 -68259.8031091165 148.1017576370548 0.1177316234407941
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1000 54.24228199265479 -68245.58589458198 133.8816957314364 0.1314999893461343
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Loop time of 4.78682 on 4 procs for 1000 steps with 16000 atoms
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Loop time of 2.16917 on 4 procs for 1000 steps with 16000 atoms
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Performance: 1.805 ns/day, 13.297 hours/ns, 208.907 timesteps/s
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100.0% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 3.983 ns/day, 6.025 hours/ns, 461.006 timesteps/s, 7.376 Matom-step/s
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97.7% 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 | 4.1562 | 4.2154 | 4.2851 | 2.7 | 88.06
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Pair | 1.8638 | 1.8826 | 1.9014 | 1.0 | 86.79
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.16658 | 0.23631 | 0.29566 | 11.5 | 4.94
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Output | 0.0016285 | 0.0016618 | 0.0017414 | 0.1 | 0.03
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Modify | 0.31425 | 0.31577 | 0.31755 | 0.2 | 6.60
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Other | | 0.01766 | | | 0.37
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Comm | 0.057938 | 0.076258 | 0.094755 | 4.8 | 3.52
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Output | 0.00020722 | 0.00022911 | 0.00029186 | 0.0 | 0.01
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Modify | 0.20222 | 0.20238 | 0.20256 | 0.0 | 9.33
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Other | | 0.007738 | | | 0.36
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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@ -116,4 +128,4 @@ Total # of neighbors = 896000
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Ave neighs/atom = 56
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:04
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Total wall time: 0:00:02
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