169 lines
5.7 KiB
Groff
169 lines
5.7 KiB
Groff
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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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 1.7320508 1
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atom_style atomic
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region box block 0 ${len} 0 ${len} -0.5 0.5
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region box block 0 4 0 ${len} -0.5 0.5
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region box block 0 4 0 4 -0.5 0.5
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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 -0.5) to (4 6.9282032 0.5)
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1 by 1 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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using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
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create_atoms CPU = 0.000 seconds
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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 with time integration, atoms won't move (src/verlet.cpp:60)
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 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) = 3.03 | 3.03 | 3.03 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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27.712813 27.712813 27.712813 3.1974423e-14 0 186 12 36 0
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Loop time of 7.96e-07 on 1 procs for 0 steps with 32 atoms
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125.6% CPU use with 1 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 | | 7.96e-07 | | |100.00
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Nlocal: 32 ave 32 max 32 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 325 ave 325 max 325 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 325
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Ave neighs/atom = 10.15625
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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 peratom and local and global quantities
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compute v2 all voronoi/atom neighbors yes edge_histo 6
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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] inputs local
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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 with time integration, atoms won't move (src/verlet.cpp:60)
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 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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171.39013 0 186 12 36 0
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Loop time of 3.74e-07 on 1 procs for 0 steps with 32 atoms
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0.0% CPU use with 1 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 | | 3.74e-07 | | |100.00
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Nlocal: 32 ave 32 max 32 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 325 ave 325 max 325 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 325
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Ave neighs/atom = 10.15625
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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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