forked from lijiext/lammps
171 lines
5.0 KiB
Groff
171 lines
5.0 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Exercise different output data options
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variable len equal 4.0
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variable lenz equal 10.0
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dimension 2
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units metal
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boundary f f p
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lattice hex 1.0 origin 0.25 0.25 0.0
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Lattice spacing in x,y,z = 1 1.73205 1
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atom_style atomic
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region box block 0 ${len} 0 ${len} 0.0 ${lenz}
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region box block 0 4 0 ${len} 0.0 ${lenz}
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region box block 0 4 0 4 0.0 ${lenz}
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region box block 0 4 0 4 0.0 10
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region atoms block 0 ${len} 0 ${len} 0.0 0.0
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region atoms block 0 4 0 ${len} 0.0 0.0
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region atoms block 0 4 0 4 0.0 0.0
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create_box 1 box
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Created orthogonal box = (0 0 0) to (4 6.9282 10)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 region atoms
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Created 32 atoms
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Time spent = 0.000311136 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 0.0 1.0
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neighbor 1.0 nsq
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#
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# TEST 1:
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#
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# This compute voronoi generates all three
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# types of quantity: per-atom, local, and global
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compute v1 all voronoi/atom neighbors yes edge_histo 6
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# write voronoi per-atom quantities to a file
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dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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# writing voronoi local quantities to a file
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dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
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# sum up a voronoi per-atom quantity
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compute volvor all reduce sum c_v1[1]
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variable volsys equal lz*lx*ly
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variable err equal c_volvor-v_volsys
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# output voronoi global quantities
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thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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thermo 1
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run 0
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WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
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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 = 3.5
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ghost atom cutoff = 3.5
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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/nsq/newton
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 9.922 | 9.922 | 9.922 Mbytes
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c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0
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Loop time of 1.40667e-05 on 4 procs for 0 steps with 32 atoms
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46.2% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 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 | | 1.407e-05 | | |100.00
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Nlocal: 8 ave 8 max 8 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 24 ave 24 max 24 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 81.25 ave 84 max 77 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 325
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Ave neighs/atom = 10.1562
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Neighbor list builds = 0
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Dangerous builds = 0
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uncompute v1
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uncompute volvor
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undump dperatom
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undump dlocal
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#
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# TEST 2:
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#
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# This compute voronoi generates
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# local and global quantities, but
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# not per-atom quantities
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compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
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# write voronoi local quantities to a file
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dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
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# sum up a voronoi local quantity
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compute sumarea all reduce sum c_v2[3]
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# output voronoi global quantities
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thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
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thermo 1
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run 0
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WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 8.671 | 8.671 | 8.671 Mbytes
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c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
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1215.0706 0 186 12 36 0
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Loop time of 2.71797e-05 on 4 procs for 0 steps with 32 atoms
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57.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 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 | | 2.718e-05 | | |100.00
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Nlocal: 8 ave 8 max 8 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 24 ave 24 max 24 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 81.25 ave 84 max 77 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 325
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Ave neighs/atom = 10.1562
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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