git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
130
examples/voronoi/log.15Feb16.voronoi.2d.g++.1
Normal file
130
examples/voronoi/log.15Feb16.voronoi.2d.g++.1
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@ -0,0 +1,130 @@
|
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LAMMPS (15 Feb 2016)
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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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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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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 (../verlet.cpp:55)
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Neighbor list info ...
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1 neighbor list requests
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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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Memory usage per processor = 2.37519 Mbytes
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volvor volsys Volume err
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277.12813 277.12813 27.712813 5.6843419e-14
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Loop time of 3.09944e-06 on 1 procs for 0 steps with 32 atoms
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0.0% 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
|
||||
---------------------------------------------------------------
|
||||
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 | | 3.099e-06 | | |100.00
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||||
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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: 2415 ave 2415 max 2415 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 8256 ave 8256 max 8256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 (../verlet.cpp:55)
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Memory usage per processor = 7.05652 Mbytes
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volvor volsys Volume err
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277.12813 277.12813 27.712813 3.4106051e-13
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Loop time of 0 on 1 procs for 0 steps with 32 atoms
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0.0% 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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---------------------------------------------------------------
|
||||
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 | | 0 | | | 0.00
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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: 496 ave 496 max 496 min
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Histogram: 1 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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130
examples/voronoi/log.15Feb16.voronoi.2d.g++.4
Normal file
130
examples/voronoi/log.15Feb16.voronoi.2d.g++.4
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@ -0,0 +1,130 @@
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LAMMPS (15 Feb 2016)
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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
|
||||
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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mass 1 1.0
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||||
|
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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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|
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neighbor ${rskin} nsq
|
||||
neighbor 2 nsq
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|
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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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|
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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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#
|
||||
|
||||
run 0
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||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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Neighbor list info ...
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||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
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||||
ghost atom cutoff = 20
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||||
Memory usage per processor = 2.41069 Mbytes
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volvor volsys Volume err
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277.12813 277.12813 27.712813 5.1159077e-13
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Loop time of 6.19888e-06 on 4 procs for 0 steps with 32 atoms
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||||
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||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
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||||
|
||||
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
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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 | | 6.199e-06 | | |100.00
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||||
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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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||||
|
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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
|
||||
#
|
||||
|
||||
change_box all boundary f f p
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||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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||||
Memory usage per processor = 7.04625 Mbytes
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||||
volvor volsys Volume err
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||||
277.12813 277.12813 27.712813 3.4106051e-13
|
||||
Loop time of 2.86102e-06 on 4 procs for 0 steps with 32 atoms
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||||
|
||||
0.0% 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
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||||
Other | | 2.861e-06 | | |100.00
|
||||
|
||||
Nlocal: 8 ave 8 max 8 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
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||||
Nghost: 24 ave 24 max 24 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 124 ave 124 max 124 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 496
|
||||
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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||||
163
examples/voronoi/log.15Feb16.voronoi.data.g++.1
Normal file
163
examples/voronoi/log.15Feb16.voronoi.data.g++.1
Normal file
@ -0,0 +1,163 @@
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LAMMPS (15 Feb 2016)
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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
|
||||
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
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (4 6.9282 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region atoms
|
||||
Created 32 atoms
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 0.0 1.0
|
||||
|
||||
neighbor 1.0 nsq
|
||||
|
||||
#
|
||||
# TEST 1:
|
||||
#
|
||||
|
||||
# This compute voronoi generates all three
|
||||
# types of quantity: per-atom, local, and global
|
||||
|
||||
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]
|
||||
|
||||
# sum up a voronoi per-atom quantity
|
||||
|
||||
compute volvor all reduce sum c_v1[1]
|
||||
|
||||
variable volsys equal lz*lx*ly
|
||||
variable err equal c_volvor-v_volsys
|
||||
|
||||
# output voronoi global quantities
|
||||
|
||||
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]
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.5
|
||||
ghost atom cutoff = 3.5
|
||||
Memory usage per processor = 9.40674 Mbytes
|
||||
volvor volsys Volume err v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0
|
||||
Loop time of 1.19209e-06 on 1 procs for 0 steps with 32 atoms
|
||||
|
||||
0.0% CPU use with 1 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 | | 1.192e-06 | | |100.00
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 325 ave 325 max 325 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 325
|
||||
Ave neighs/atom = 10.1562
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
uncompute v1
|
||||
uncompute volvor
|
||||
undump dperatom
|
||||
undump dlocal
|
||||
|
||||
#
|
||||
# TEST 2:
|
||||
#
|
||||
|
||||
# This compute voronoi generates
|
||||
# local and global quantities, but
|
||||
# not per-atom quantities
|
||||
|
||||
compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
|
||||
|
||||
# write voronoi local quantities to a file
|
||||
|
||||
dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
|
||||
|
||||
# sum up a voronoi local quantity
|
||||
|
||||
compute sumarea all reduce sum c_v2[3]
|
||||
|
||||
# output voronoi global quantities
|
||||
|
||||
thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 8.15503 Mbytes
|
||||
sumarea v2[3] v2[4] v2[5] v2[6] v2[7]
|
||||
1215.0706 0 186 12 36 0
|
||||
Loop time of 0 on 1 procs for 0 steps with 32 atoms
|
||||
|
||||
0.0% CPU use with 1 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 | | 0 | | | 0.00
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 325 ave 325 max 325 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 325
|
||||
Ave neighs/atom = 10.1562
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
163
examples/voronoi/log.15Feb16.voronoi.data.g++.4
Normal file
163
examples/voronoi/log.15Feb16.voronoi.data.g++.4
Normal file
@ -0,0 +1,163 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# Exercise different output data options
|
||||
|
||||
variable len equal 4.0
|
||||
variable lenz equal 10.0
|
||||
|
||||
dimension 2
|
||||
units metal
|
||||
boundary f f p
|
||||
|
||||
lattice hex 1.0 origin 0.25 0.25 0.0
|
||||
Lattice spacing in x,y,z = 1 1.73205 1
|
||||
|
||||
atom_style atomic
|
||||
|
||||
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
|
||||
region box block 0 4 0 ${len} 0.0 ${lenz}
|
||||
region box block 0 4 0 4 0.0 ${lenz}
|
||||
region box block 0 4 0 4 0.0 10
|
||||
region atoms block 0 ${len} 0 ${len} 0.0 0.0
|
||||
region atoms block 0 4 0 ${len} 0.0 0.0
|
||||
region atoms block 0 4 0 4 0.0 0.0
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (4 6.9282 10)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region atoms
|
||||
Created 32 atoms
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 0.0 1.0
|
||||
|
||||
neighbor 1.0 nsq
|
||||
|
||||
#
|
||||
# TEST 1:
|
||||
#
|
||||
|
||||
# This compute voronoi generates all three
|
||||
# types of quantity: per-atom, local, and global
|
||||
|
||||
compute v1 all voronoi/atom neighbors yes edge_histo 6
|
||||
|
||||
# write voronoi per-atom quantities to a file
|
||||
|
||||
dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
|
||||
# writing voronoi local quantities to a file
|
||||
|
||||
dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
|
||||
|
||||
# sum up a voronoi per-atom quantity
|
||||
|
||||
compute volvor all reduce sum c_v1[1]
|
||||
|
||||
variable volsys equal lz*lx*ly
|
||||
variable err equal c_volvor-v_volsys
|
||||
|
||||
# output voronoi global quantities
|
||||
|
||||
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]
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.5
|
||||
ghost atom cutoff = 3.5
|
||||
Memory usage per processor = 9.29039 Mbytes
|
||||
volvor volsys Volume err v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0
|
||||
Loop time of 3.99351e-06 on 4 procs for 0 steps with 32 atoms
|
||||
|
||||
0.0% 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 | | 3.994e-06 | | |100.00
|
||||
|
||||
Nlocal: 8 ave 8 max 8 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 24 ave 24 max 24 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 81.25 ave 84 max 77 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 325
|
||||
Ave neighs/atom = 10.1562
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
uncompute v1
|
||||
uncompute volvor
|
||||
undump dperatom
|
||||
undump dlocal
|
||||
|
||||
#
|
||||
# TEST 2:
|
||||
#
|
||||
|
||||
# This compute voronoi generates
|
||||
# local and global quantities, but
|
||||
# not per-atom quantities
|
||||
|
||||
compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
|
||||
|
||||
# write voronoi local quantities to a file
|
||||
|
||||
dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
|
||||
|
||||
# sum up a voronoi local quantity
|
||||
|
||||
compute sumarea all reduce sum c_v2[3]
|
||||
|
||||
# output voronoi global quantities
|
||||
|
||||
thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 8.03996 Mbytes
|
||||
sumarea v2[3] v2[4] v2[5] v2[6] v2[7]
|
||||
1215.0706 0 186 12 36 0
|
||||
Loop time of 2.86102e-06 on 4 procs for 0 steps with 32 atoms
|
||||
|
||||
0.0% 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 | | 2.861e-06 | | |100.00
|
||||
|
||||
Nlocal: 8 ave 8 max 8 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 24 ave 24 max 24 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 81.25 ave 84 max 77 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 325
|
||||
Ave neighs/atom = 10.1562
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
619
examples/voronoi/log.15Feb16.voronoi.g++.1
Normal file
619
examples/voronoi/log.15Feb16.voronoi.g++.1
Normal file
@ -0,0 +1,619 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# Test of Kawasaki Dynamics on LJ test system
|
||||
|
||||
units metal
|
||||
#newton off
|
||||
boundary p p p
|
||||
|
||||
lattice fcc 1 origin 0.25 0.25 0.25
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
atom_style atomic
|
||||
|
||||
# indexed atom variables in test 5 need a map
|
||||
|
||||
atom_modify sort 0 0.0 map hash
|
||||
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 2
|
||||
Created 4000 atoms
|
||||
|
||||
mass 1 50
|
||||
mass 2 50
|
||||
|
||||
pair_style lj/cut 2.0
|
||||
pair_coeff 1 1 0.0 1.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
# set the cut-off to 2.5x the cutoff from the potential
|
||||
comm_modify cutoff 5.0
|
||||
|
||||
# atom radii per type
|
||||
variable r atom (type==1)*0.1+(type==2)*0.3
|
||||
|
||||
# groups
|
||||
group type1 type 1
|
||||
3000 atoms in group type1
|
||||
group type2 type 2
|
||||
1000 atoms in group type2
|
||||
|
||||
thermo 1
|
||||
# reduce computes
|
||||
#compute r1 type1 reduce sum c_v1[1]
|
||||
#compute r2 type2 reduce sum c_v1[1]
|
||||
|
||||
#compute v1 all voronoi/atom radius v_r
|
||||
|
||||
#
|
||||
# TEST 1: Sum of all voronoi cells is the simulation cell volume
|
||||
#
|
||||
|
||||
compute v1 all voronoi/atom
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
thermo_style custom c_r0
|
||||
variable t1 equal c_r0
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.3
|
||||
ghost atom cutoff = 5
|
||||
binsize = 1.15 -> bins = 9 9 9
|
||||
Memory usage per processor = 8.24398 Mbytes
|
||||
r0
|
||||
1000
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 1 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 | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume"
|
||||
TEST_1 0% Error. Sum of all voronoi cells is the simulation cell volume
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
undump d1
|
||||
|
||||
#
|
||||
# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume
|
||||
#
|
||||
|
||||
compute v1 type2 voronoi/atom only_group
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 type2 reduce sum c_v1[1]
|
||||
compute r1 type1 reduce sum c_v1[1]
|
||||
thermo_style custom c_r0 c_r1
|
||||
variable t2a equal c_r0
|
||||
variable t2b equal c_r1
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 8.24398 Mbytes
|
||||
r0 r1
|
||||
1000 0
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 1 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 | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume"
|
||||
TEST_2a 0% Error. Sum of all only_group voronoi cells is the simulation cell volume
|
||||
print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero"
|
||||
TEST_2b 0% Error. Sum of all only_group not included voronoi cells is zero
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
uncompute r1
|
||||
undump d1
|
||||
|
||||
#
|
||||
# TEST 3: Sum of all radius voronoi cells is the simulation cell volume
|
||||
#
|
||||
|
||||
compute v1 all voronoi/atom radius v_r
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
thermo_style custom c_r0
|
||||
variable t3 equal c_r0
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 8.24398 Mbytes
|
||||
r0
|
||||
1000
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 1 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 | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume"
|
||||
TEST_3 0% Error. Sum of all radius voronoi cells is the simulation cell volume
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
undump d1
|
||||
|
||||
#
|
||||
# TEST 4: Edge histogram tests
|
||||
#
|
||||
|
||||
compute v1 type2 voronoi/atom edge_histo 8
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.03036 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 12000 0 0 0
|
||||
0 0 0 12000 0 0 0
|
||||
Loop time of 0.454023 on 1 procs for 1 steps with 4000 atoms
|
||||
|
||||
Performance: 0.190 ns/day, 126.118 hours/ns, 2.203 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0059121 | 0.0059121 | 0.0059121 | 0.0 | 1.30
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00020099 | 0.00020099 | 0.00020099 | 0.0 | 0.04
|
||||
Output | 0.44782 | 0.44782 | 0.44782 | 0.0 | 98.63
|
||||
Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
|
||||
Other | | 8.702e-05 | | | 0.02
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120
|
||||
print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)"
|
||||
TEST_4a 0% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)
|
||||
uncompute v1
|
||||
compute v1 all voronoi/atom edge_histo 8
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.03036 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 48000 0 0 0
|
||||
0 0 0 48000 0 0 0
|
||||
Loop time of 0.473173 on 1 procs for 1 steps with 4000 atoms
|
||||
|
||||
Performance: 0.183 ns/day, 131.437 hours/ns, 2.113 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.005954 | 0.005954 | 0.005954 | 0.0 | 1.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0002439 | 0.0002439 | 0.0002439 | 0.0 | 0.05
|
||||
Output | 0.46687 | 0.46687 | 0.46687 | 0.0 | 98.67
|
||||
Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
|
||||
Other | | 0.0001042 | | | 0.02
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4b equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
|
||||
print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)"
|
||||
TEST_4b 0% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)
|
||||
uncompute v1
|
||||
|
||||
# perturbed fcc lattice
|
||||
displace_atoms all random 0.01 0.01 0.01 31423
|
||||
compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.03036 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 48000 0 0 0
|
||||
0 0 0 48000 0 0 0
|
||||
Loop time of 0.471937 on 1 procs for 1 steps with 4000 atoms
|
||||
|
||||
Performance: 0.183 ns/day, 131.094 hours/ns, 2.119 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0062199 | 0.0062199 | 0.0062199 | 0.0 | 1.32
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00022388 | 0.00022388 | 0.00022388 | 0.0 | 0.05
|
||||
Output | 0.46539 | 0.46539 | 0.46539 | 0.0 | 98.61
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.823e-05 | | | 0.02
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4c equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
|
||||
print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold"
|
||||
TEST_4c 0% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold
|
||||
uncompute v1
|
||||
|
||||
# bcc lattice
|
||||
delete_atoms group all
|
||||
Deleted 4000 atoms, new total = 0
|
||||
lattice bcc 1 origin 0.25 0.25 0.25
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
create_atoms 1 box
|
||||
Created 2000 atoms
|
||||
compute v1 all voronoi/atom edge_histo 8
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.03036 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 12000 0 16000 0
|
||||
0 0 0 12000 0 16000 0
|
||||
Loop time of 0.211795 on 1 procs for 1 steps with 2000 atoms
|
||||
|
||||
Performance: 0.408 ns/day, 58.832 hours/ns, 4.722 timesteps/s
|
||||
100.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0014911 | 0.0014911 | 0.0014911 | 0.0 | 0.70
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 8.9884e-05 | 8.9884e-05 | 8.9884e-05 | 0.0 | 0.04
|
||||
Output | 0.21018 | 0.21018 | 0.21018 | 0.0 | 99.24
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.695e-05 | | | 0.02
|
||||
|
||||
Nlocal: 2000 ave 2000 max 2000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 14000 ave 14000 max 14000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 112000 ave 112000 max 112000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 112000
|
||||
Ave neighs/atom = 56
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4d equal (abs(c_v1[4]-12000)+abs(c_v1[6]-16000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[7])/280
|
||||
print "TEST_4d $(round(v_t4d))% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)"
|
||||
TEST_4d 0% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)
|
||||
uncompute v1
|
||||
|
||||
# restore fcc lattice
|
||||
delete_atoms group all
|
||||
Deleted 2000 atoms, new total = 0
|
||||
lattice fcc 1 origin 0.25 0.25 0.25
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
create_atoms 1 box basis 1 2
|
||||
Created 4000 atoms
|
||||
|
||||
#
|
||||
# TEST 5: Occupation analysis
|
||||
#
|
||||
|
||||
print "START5"
|
||||
START5
|
||||
|
||||
# start with pristine lattice
|
||||
variable i1 equal 13
|
||||
variable i2 equal 257
|
||||
compute v1 all voronoi/atom occupation
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
compute r1 all reduce sum c_v1[2]
|
||||
variable d5a equal c_v1[${i1}][1]
|
||||
variable d5a equal c_v1[13][1]
|
||||
variable d5b equal c_v1[${i2}][1]
|
||||
variable d5b equal c_v1[257][1]
|
||||
variable d5c equal c_v1[${i1}][2]
|
||||
variable d5c equal c_v1[13][2]
|
||||
variable d5d equal c_v1[${i2}][2]
|
||||
variable d5d equal c_v1[257][2]
|
||||
thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.03036 Mbytes
|
||||
r0 r1 d5a d5b d5c d5d
|
||||
4000 4000 1 1 1 1
|
||||
Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.192e-06 | | |100.00
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
# expect 1 1 1 1 (one atom per cell each)
|
||||
variable t5a equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
|
||||
|
||||
# move atom i1 next to atom i2
|
||||
variable oxd equal x[${i1}]
|
||||
variable oxd equal x[13]
|
||||
variable oyd equal y[${i1}]
|
||||
variable oyd equal y[13]
|
||||
variable ozd equal z[${i1}]
|
||||
variable ozd equal z[13]
|
||||
# we need to freeze this value
|
||||
variable ox equal ${oxd}
|
||||
variable ox equal 3.25
|
||||
variable oy equal ${oyd}
|
||||
variable oy equal 0.25
|
||||
variable oz equal ${ozd}
|
||||
variable oz equal 0.25
|
||||
# these coords dont change so dynamic evaluation is ok
|
||||
variable nx equal x[${i2}]
|
||||
variable nx equal x[257]
|
||||
variable ny equal y[${i2}]
|
||||
variable ny equal y[257]
|
||||
variable nz equal z[${i2}]
|
||||
variable nz equal z[257]
|
||||
set atom ${i1} x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
|
||||
set atom 13 x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
|
||||
set atom 13 x 4.4500000000000001776 y $(v_ny+0.2) z $(v_nz+0.2)
|
||||
set atom 13 x 4.4500000000000001776 y 6.4500000000000001776 z $(v_nz+0.2)
|
||||
set atom 13 x 4.4500000000000001776 y 6.4500000000000001776 z 0.4500000000000000111
|
||||
1 settings made for x
|
||||
1 settings made for y
|
||||
1 settings made for z
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.53036 Mbytes
|
||||
r0 r1 d5a d5b d5c d5d
|
||||
4000 4002 0 2 2 2
|
||||
Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.192e-06 | | |100.00
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 399998 ave 399998 max 399998 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 399998
|
||||
Ave neighs/atom = 99.9995
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
|
||||
variable t5b equal abs(${d5a}-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(2-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(2-2)
|
||||
|
||||
# move atom back
|
||||
set atom ${i1} x ${ox} y ${oy} z ${oz}
|
||||
set atom 13 x ${ox} y ${oy} z ${oz}
|
||||
set atom 13 x 3.25 y ${oy} z ${oz}
|
||||
set atom 13 x 3.25 y 0.25 z ${oz}
|
||||
set atom 13 x 3.25 y 0.25 z 0.25
|
||||
1 settings made for x
|
||||
1 settings made for y
|
||||
1 settings made for z
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.53036 Mbytes
|
||||
r0 r1 d5a d5b d5c d5d
|
||||
4000 4000 1 1 1 1
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 28000 ave 28000 max 28000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 400000 ave 400000 max 400000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
# expect 1 1 1 1 (restored to the initial state)
|
||||
variable t5c equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
|
||||
|
||||
print "TEST_5 $((v_t5a+v_t5b+v_t5c)*100)% Error. Detection of vacancies and interstitials using the {occupation} keyword."
|
||||
TEST_5 0% Error. Detection of vacancies and interstitials using the {occupation} keyword.
|
||||
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
uncompute r1
|
||||
|
||||
#
|
||||
# TEST 6: Sum of all voronoi cells is the triclinic simulation cell volume
|
||||
#
|
||||
|
||||
# switch to triclinic box
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (10 10 10) with tilt (0 0 0)
|
||||
change_box all xy final 5.0 remap units box
|
||||
triclinic box = (0 0 0) to (10 10 10) with tilt (5 0 0)
|
||||
|
||||
compute v1 all voronoi/atom
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
thermo_style custom c_r0
|
||||
variable t6 equal c_r0
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.3
|
||||
ghost atom cutoff = 5
|
||||
binsize = 1.15 -> bins = 14 9 9
|
||||
Memory usage per processor = 11.5794 Mbytes
|
||||
r0
|
||||
1000
|
||||
Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 1 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 | | 1.192e-06 | | |100.00
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 29600 ave 29600 max 29600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 432000 ave 432000 max 432000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 432000
|
||||
Ave neighs/atom = 108
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_6 $(round((v_t6-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume"
|
||||
TEST_6 0% Error. Sum of all voronoi cells is the triclinic simulation cell volume
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
undump d1
|
||||
|
||||
# All tests done
|
||||
|
||||
print TEST_DONE
|
||||
TEST_DONE
|
||||
Total wall time: 0:00:30
|
||||
619
examples/voronoi/log.15Feb16.voronoi.g++.4
Normal file
619
examples/voronoi/log.15Feb16.voronoi.g++.4
Normal file
@ -0,0 +1,619 @@
|
||||
LAMMPS (15 Feb 2016)
|
||||
# Test of Kawasaki Dynamics on LJ test system
|
||||
|
||||
units metal
|
||||
#newton off
|
||||
boundary p p p
|
||||
|
||||
lattice fcc 1 origin 0.25 0.25 0.25
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
atom_style atomic
|
||||
|
||||
# indexed atom variables in test 5 need a map
|
||||
|
||||
atom_modify sort 0 0.0 map hash
|
||||
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 2
|
||||
Created 4000 atoms
|
||||
|
||||
mass 1 50
|
||||
mass 2 50
|
||||
|
||||
pair_style lj/cut 2.0
|
||||
pair_coeff 1 1 0.0 1.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
# set the cut-off to 2.5x the cutoff from the potential
|
||||
comm_modify cutoff 5.0
|
||||
|
||||
# atom radii per type
|
||||
variable r atom (type==1)*0.1+(type==2)*0.3
|
||||
|
||||
# groups
|
||||
group type1 type 1
|
||||
3000 atoms in group type1
|
||||
group type2 type 2
|
||||
1000 atoms in group type2
|
||||
|
||||
thermo 1
|
||||
# reduce computes
|
||||
#compute r1 type1 reduce sum c_v1[1]
|
||||
#compute r2 type2 reduce sum c_v1[1]
|
||||
|
||||
#compute v1 all voronoi/atom radius v_r
|
||||
|
||||
#
|
||||
# TEST 1: Sum of all voronoi cells is the simulation cell volume
|
||||
#
|
||||
|
||||
compute v1 all voronoi/atom
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
thermo_style custom c_r0
|
||||
variable t1 equal c_r0
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.3
|
||||
ghost atom cutoff = 5
|
||||
binsize = 1.15 -> bins = 9 9 9
|
||||
Memory usage per processor = 7.70003 Mbytes
|
||||
r0
|
||||
1000
|
||||
Loop time of 5.96046e-06 on 4 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% 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 | | 5.96e-06 | | |100.00
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100000 max 100000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume"
|
||||
TEST_1 0% Error. Sum of all voronoi cells is the simulation cell volume
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
undump d1
|
||||
|
||||
#
|
||||
# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume
|
||||
#
|
||||
|
||||
compute v1 type2 voronoi/atom only_group
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 type2 reduce sum c_v1[1]
|
||||
compute r1 type1 reduce sum c_v1[1]
|
||||
thermo_style custom c_r0 c_r1
|
||||
variable t2a equal c_r0
|
||||
variable t2b equal c_r1
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 7.70003 Mbytes
|
||||
r0 r1
|
||||
1000 0
|
||||
Loop time of 3.09944e-06 on 4 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% 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 | | 3.099e-06 | | |100.00
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100000 max 100000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume"
|
||||
TEST_2a 0% Error. Sum of all only_group voronoi cells is the simulation cell volume
|
||||
print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero"
|
||||
TEST_2b 0% Error. Sum of all only_group not included voronoi cells is zero
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
uncompute r1
|
||||
undump d1
|
||||
|
||||
#
|
||||
# TEST 3: Sum of all radius voronoi cells is the simulation cell volume
|
||||
#
|
||||
|
||||
compute v1 all voronoi/atom radius v_r
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
thermo_style custom c_r0
|
||||
variable t3 equal c_r0
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 7.70003 Mbytes
|
||||
r0
|
||||
1000
|
||||
Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% 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 | | 2.861e-06 | | |100.00
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100000 max 100000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume"
|
||||
TEST_3 0% Error. Sum of all radius voronoi cells is the simulation cell volume
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
undump d1
|
||||
|
||||
#
|
||||
# TEST 4: Edge histogram tests
|
||||
#
|
||||
|
||||
compute v1 type2 voronoi/atom edge_histo 8
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 5.64663 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 12000 0 0 0
|
||||
0 0 0 12000 0 0 0
|
||||
Loop time of 0.262419 on 4 procs for 1 steps with 4000 atoms
|
||||
|
||||
Performance: 0.329 ns/day, 72.894 hours/ns, 3.811 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0015318 | 0.0015455 | 0.0015759 | 0.0 | 0.59
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00056005 | 0.00060356 | 0.00064278 | 0.2 | 0.23
|
||||
Output | 0.26013 | 0.26017 | 0.2602 | 0.0 | 99.14
|
||||
Modify | 0 | 1.2517e-06 | 2.1458e-06 | 0.1 | 0.00
|
||||
Other | | 9.871e-05 | | | 0.04
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100000 max 100000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120
|
||||
print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)"
|
||||
TEST_4a 0% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)
|
||||
uncompute v1
|
||||
compute v1 all voronoi/atom edge_histo 8
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 5.64663 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 48000 0 0 0
|
||||
0 0 0 48000 0 0 0
|
||||
Loop time of 0.27636 on 4 procs for 1 steps with 4000 atoms
|
||||
|
||||
Performance: 0.313 ns/day, 76.767 hours/ns, 3.618 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0015159 | 0.001533 | 0.001559 | 0.0 | 0.55
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00051785 | 0.00055867 | 0.00060701 | 0.1 | 0.20
|
||||
Output | 0.27416 | 0.2742 | 0.27422 | 0.0 | 99.22
|
||||
Modify | 0 | 1.0729e-06 | 1.9073e-06 | 0.1 | 0.00
|
||||
Other | | 6.926e-05 | | | 0.03
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100000 max 100000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4b equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
|
||||
print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)"
|
||||
TEST_4b 0% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)
|
||||
uncompute v1
|
||||
|
||||
# perturbed fcc lattice
|
||||
displace_atoms all random 0.01 0.01 0.01 31423
|
||||
compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 5.64663 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 48000 0 0 0
|
||||
0 0 0 48000 0 0 0
|
||||
Loop time of 0.272119 on 4 procs for 1 steps with 4000 atoms
|
||||
|
||||
Performance: 0.318 ns/day, 75.589 hours/ns, 3.675 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 | 0.0015891 | 0.0015998 | 0.0016181 | 0.0 | 0.59
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00053191 | 0.00055522 | 0.00059175 | 0.1 | 0.20
|
||||
Output | 0.26986 | 0.2699 | 0.26992 | 0.0 | 99.18
|
||||
Modify | 0 | 2.3842e-07 | 9.5367e-07 | 0.1 | 0.00
|
||||
Other | | 6.658e-05 | | | 0.02
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100016 max 99984 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4c equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480
|
||||
print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold"
|
||||
TEST_4c 0% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold
|
||||
uncompute v1
|
||||
|
||||
# bcc lattice
|
||||
delete_atoms group all
|
||||
Deleted 4000 atoms, new total = 0
|
||||
lattice bcc 1 origin 0.25 0.25 0.25
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
create_atoms 1 box
|
||||
Created 2000 atoms
|
||||
compute v1 all voronoi/atom edge_histo 8
|
||||
thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 5.64663 Mbytes
|
||||
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
|
||||
0 0 0 12000 0 16000 0
|
||||
0 0 0 12000 0 16000 0
|
||||
Loop time of 0.120695 on 4 procs for 1 steps with 2000 atoms
|
||||
|
||||
Performance: 0.716 ns/day, 33.526 hours/ns, 8.285 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00037694 | 0.00038201 | 0.00039315 | 0.0 | 0.32
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00030208 | 0.00031257 | 0.00033903 | 0.1 | 0.26
|
||||
Output | 0.11993 | 0.11996 | 0.11997 | 0.0 | 99.39
|
||||
Modify | 0 | 7.1526e-07 | 1.9073e-06 | 0.1 | 0.00
|
||||
Other | | 4.16e-05 | | | 0.03
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8500 ave 8500 max 8500 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28000 ave 28000 max 28000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 112000
|
||||
Ave neighs/atom = 56
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
variable t4d equal (abs(c_v1[4]-12000)+abs(c_v1[6]-16000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[7])/280
|
||||
print "TEST_4d $(round(v_t4d))% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)"
|
||||
TEST_4d 0% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)
|
||||
uncompute v1
|
||||
|
||||
# restore fcc lattice
|
||||
delete_atoms group all
|
||||
Deleted 2000 atoms, new total = 0
|
||||
lattice fcc 1 origin 0.25 0.25 0.25
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
create_atoms 1 box basis 1 2
|
||||
Created 4000 atoms
|
||||
|
||||
#
|
||||
# TEST 5: Occupation analysis
|
||||
#
|
||||
|
||||
print "START5"
|
||||
START5
|
||||
|
||||
# start with pristine lattice
|
||||
variable i1 equal 13
|
||||
variable i2 equal 257
|
||||
compute v1 all voronoi/atom occupation
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
compute r1 all reduce sum c_v1[2]
|
||||
variable d5a equal c_v1[${i1}][1]
|
||||
variable d5a equal c_v1[13][1]
|
||||
variable d5b equal c_v1[${i2}][1]
|
||||
variable d5b equal c_v1[257][1]
|
||||
variable d5c equal c_v1[${i1}][2]
|
||||
variable d5c equal c_v1[13][2]
|
||||
variable d5d equal c_v1[${i2}][2]
|
||||
variable d5d equal c_v1[257][2]
|
||||
thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 5.64663 Mbytes
|
||||
r0 r1 d5a d5b d5c d5d
|
||||
4000 4000 1 1 1 1
|
||||
Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.861e-06 | | |100.00
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100000 max 100000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
# expect 1 1 1 1 (one atom per cell each)
|
||||
variable t5a equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
|
||||
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
|
||||
|
||||
# move atom i1 next to atom i2
|
||||
variable oxd equal x[${i1}]
|
||||
variable oxd equal x[13]
|
||||
variable oyd equal y[${i1}]
|
||||
variable oyd equal y[13]
|
||||
variable ozd equal z[${i1}]
|
||||
variable ozd equal z[13]
|
||||
# we need to freeze this value
|
||||
variable ox equal ${oxd}
|
||||
variable ox equal 3.25
|
||||
variable oy equal ${oyd}
|
||||
variable oy equal 0.25
|
||||
variable oz equal ${ozd}
|
||||
variable oz equal 0.25
|
||||
# these coords dont change so dynamic evaluation is ok
|
||||
variable nx equal x[${i2}]
|
||||
variable nx equal x[257]
|
||||
variable ny equal y[${i2}]
|
||||
variable ny equal y[257]
|
||||
variable nz equal z[${i2}]
|
||||
variable nz equal z[257]
|
||||
set atom ${i1} x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
|
||||
set atom 13 x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
|
||||
set atom 13 x 4.4500000000000001776 y $(v_ny+0.2) z $(v_nz+0.2)
|
||||
set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z $(v_nz+0.2)
|
||||
set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z 1.4499999999999999556
|
||||
1 settings made for x
|
||||
1 settings made for y
|
||||
1 settings made for z
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.14663 Mbytes
|
||||
r0 r1 d5a d5b d5c d5d
|
||||
4000 4002 0 2 2 2
|
||||
Loop time of 2.74181e-06 on 4 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.742e-06 | | |100.00
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 99999.2 ave 100075 max 99967 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 399997
|
||||
Ave neighs/atom = 99.9993
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
|
||||
variable t5b equal abs(${d5a}-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(2-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(${d5d}-2)
|
||||
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(2-2)
|
||||
|
||||
# move atom back
|
||||
set atom ${i1} x ${ox} y ${oy} z ${oz}
|
||||
set atom 13 x ${ox} y ${oy} z ${oz}
|
||||
set atom 13 x 3.25 y ${oy} z ${oz}
|
||||
set atom 13 x 3.25 y 0.25 z ${oz}
|
||||
set atom 13 x 3.25 y 0.25 z 0.25
|
||||
1 settings made for x
|
||||
1 settings made for y
|
||||
1 settings made for z
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Memory usage per processor = 6.14663 Mbytes
|
||||
r0 r1 d5a d5b d5c d5d
|
||||
4000 4000 1 1 1 1
|
||||
Loop time of 2.6226e-06 on 4 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.623e-06 | | |100.00
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17000 ave 17000 max 17000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100000 ave 100000 max 100000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 400000
|
||||
Ave neighs/atom = 100
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
# expect 1 1 1 1 (restored to the initial state)
|
||||
variable t5c equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
|
||||
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
|
||||
|
||||
print "TEST_5 $((v_t5a+v_t5b+v_t5c)*100)% Error. Detection of vacancies and interstitials using the {occupation} keyword."
|
||||
TEST_5 0% Error. Detection of vacancies and interstitials using the {occupation} keyword.
|
||||
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
uncompute r1
|
||||
|
||||
#
|
||||
# TEST 6: Sum of all voronoi cells is the triclinic simulation cell volume
|
||||
#
|
||||
|
||||
# switch to triclinic box
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (10 10 10) with tilt (0 0 0)
|
||||
change_box all xy final 5.0 remap units box
|
||||
triclinic box = (0 0 0) to (10 10 10) with tilt (5 0 0)
|
||||
|
||||
compute v1 all voronoi/atom
|
||||
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
||||
compute r0 all reduce sum c_v1[1]
|
||||
thermo_style custom c_r0
|
||||
variable t6 equal c_r0
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.3
|
||||
ghost atom cutoff = 5
|
||||
binsize = 1.15 -> bins = 14 9 9
|
||||
Memory usage per processor = 7.70784 Mbytes
|
||||
r0
|
||||
250
|
||||
Loop time of 4.29153e-06 on 4 procs for 0 steps with 4000 atoms
|
||||
|
||||
0.0% 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 | | 4.292e-06 | | |100.00
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 17900 ave 17900 max 17900 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 108000 ave 108000 max 108000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 432000
|
||||
Ave neighs/atom = 108
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
print "TEST_6 $(round((v_t6-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume"
|
||||
TEST_6 -75% Error. Sum of all voronoi cells is the triclinic simulation cell volume
|
||||
uncompute v1
|
||||
uncompute r0
|
||||
undump d1
|
||||
|
||||
# All tests done
|
||||
|
||||
print TEST_DONE
|
||||
TEST_DONE
|
||||
Total wall time: 0:00:11
|
||||
Reference in New Issue
Block a user