forked from lijiext/lammps
138 lines
4.3 KiB
Groff
138 lines
4.3 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Test volume definitions for 2d and finite systems
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variable rcut equal 10.0
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variable rskin equal 2.0
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variable rcomm equal 20.0
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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 p p p
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#lattice sq 1.0 origin 0.5 0.5 0.0
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lattice hex 1.0 origin 0.5 0.5 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 = 0.000319481 secs
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mass 1 1.0
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pair_style lj/cut ${rcut}
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pair_style lj/cut 10
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pair_coeff 1 1 0.0 1.0
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neighbor ${rskin} nsq
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neighbor 2 nsq
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# set the minimum communication cut-off
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comm_modify cutoff ${rcomm}
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comm_modify cutoff 20
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compute v1 all voronoi/atom neighbors yes
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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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thermo_style custom c_volvor v_volsys vol v_err
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thermo 1
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#
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# TEST 1: Volume check for 2d bulk system
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#
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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 = 12
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ghost atom cutoff = 20
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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) = 3.042 | 3.042 | 3.042 Mbytes
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c_volvor v_volsys Volume v_err
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277.12813 277.12813 27.712813 5.1159077e-13
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Loop time of 2.79546e-05 on 4 procs for 0 steps with 32 atoms
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51.9% 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 | | 2.795e-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: 2159 ave 2159 max 2159 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 2064 ave 2077 max 2051 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 8256
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Ave neighs/atom = 258
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Neighbor list builds = 0
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Dangerous builds = 0
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#
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# TEST 2: Volume check for 2d finite system
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# add margins in x and y directions
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#
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change_box all boundary f f p
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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) = 7.678 | 7.678 | 7.678 Mbytes
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c_volvor v_volsys Volume v_err
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277.12813 277.12813 27.712813 3.4106051e-13
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Loop time of 1.88947e-05 on 4 procs for 0 steps with 32 atoms
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47.6% 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 | | 1.889e-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: 124 ave 124 max 124 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 496
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Ave neighs/atom = 15.5
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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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