make 2d system box center on 0.0
This commit is contained in:
Axel Kohlmeyer
@ -7,46 +7,46 @@ variable len equal 4.0
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variable lenz equal 10.0
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variable lenz equal 10.0
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dimension 2
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dimension 2
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units metal
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units metal
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boundary p p p
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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 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 hex 1.0 origin 0.5 0.5 0.0
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atom_style atomic
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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 ${len} 0 ${len} -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 ${len} 0 ${len} 0.0 0.0
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create_box 1 box
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create_box 1 box
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create_atoms 1 region atoms
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create_atoms 1 region atoms
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mass 1 1.0
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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 ${rcut}
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pair_coeff 1 1 0.0 1.0
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pair_coeff 1 1 0.0 1.0
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neighbor ${rskin} nsq
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neighbor ${rskin} nsq
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# set the minimum communication cut-off
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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 ${rcomm}
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compute v1 all voronoi/atom neighbors yes
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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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compute volvor all reduce sum c_v1[1]
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variable volsys equal lz*lx*ly
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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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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_style custom c_volvor v_volsys vol v_err
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thermo 1
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thermo 1
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#
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#
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# TEST 1: Volume check for 2d bulk system
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# TEST 1: Volume check for 2d bulk system
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#
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#
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run 0
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run 0
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#
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#
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# TEST 2: Volume check for 2d finite system
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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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# add margins in x and y directions
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#
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#
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change_box all boundary f f p
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change_box all boundary f f p
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run 0
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run 0
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@ -4,24 +4,24 @@ variable len equal 4.0
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variable lenz equal 10.0
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variable lenz equal 10.0
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dimension 2
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dimension 2
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units metal
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units metal
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boundary f f p
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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 hex 1.0 origin 0.25 0.25 0.0
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atom_style atomic
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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 ${len} 0 ${len} -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 ${len} 0 ${len} 0.0 0.0
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create_box 1 box
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create_box 1 box
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create_atoms 1 region atoms
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create_atoms 1 region atoms
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mass 1 1.0
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mass 1 1.0
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pair_style lj/cut 2.5
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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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pair_coeff 1 1 0.0 1.0
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neighbor 1.0 nsq
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neighbor 1.0 nsq
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#
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#
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# TEST 1:
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# TEST 1:
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@ -30,11 +30,11 @@ neighbor 1.0 nsq
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# This compute voronoi generates all three
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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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# 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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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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# 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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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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# writing voronoi local quantities to a file
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@ -42,17 +42,17 @@ 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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# sum up a voronoi per-atom quantity
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compute volvor all reduce sum c_v1[1]
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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 volsys equal lz*lx*ly
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variable err equal c_volvor-v_volsys
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variable err equal c_volvor-v_volsys
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# output voronoi global quantities
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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_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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thermo 1
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run 0
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run 0
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uncompute v1
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uncompute v1
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uncompute volvor
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uncompute volvor
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@ -65,7 +65,7 @@ undump dlocal
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# This compute voronoi generates peratom and local and global quantities
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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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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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# write voronoi local quantities to a file
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@ -73,11 +73,11 @@ 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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# sum up a voronoi local quantity
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compute sumarea all reduce sum c_v2[3] inputs local
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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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# 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_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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thermo 1
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run 0
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run 0
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@ -1,170 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Exercise different output data options
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variable len equal 4.0
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variable lenz equal 10.0
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dimension 2
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units metal
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boundary f f p
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lattice hex 1.0 origin 0.25 0.25 0.0
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Lattice spacing in x,y,z = 1 1.73205 1
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atom_style atomic
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region box block 0 ${len} 0 ${len} 0.0 ${lenz}
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region box block 0 4 0 ${len} 0.0 ${lenz}
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region box block 0 4 0 4 0.0 ${lenz}
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region box block 0 4 0 4 0.0 10
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region atoms block 0 ${len} 0 ${len} 0.0 0.0
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region atoms block 0 4 0 ${len} 0.0 0.0
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region atoms block 0 4 0 4 0.0 0.0
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create_box 1 box
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Created orthogonal box = (0 0 0) to (4 6.9282 10)
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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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Time spent = 0.000315666 secs
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 0.0 1.0
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neighbor 1.0 nsq
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#
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# TEST 1:
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#
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# This compute voronoi generates all three
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# types of quantity: per-atom, local, and global
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compute v1 all voronoi/atom neighbors yes edge_histo 6
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# write voronoi per-atom quantities to a file
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dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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# writing voronoi local quantities to a file
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dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
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# sum up a voronoi per-atom quantity
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compute volvor all reduce sum c_v1[1]
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variable volsys equal lz*lx*ly
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variable err equal c_volvor-v_volsys
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# output voronoi global quantities
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thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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thermo 1
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run 0
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WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.5
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ghost atom cutoff = 3.5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/nsq/newton
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 10.04 | 10.04 | 10.04 Mbytes
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c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0
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Loop time of 7.15256e-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 | | 7.153e-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 = 10.1562
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Neighbor list builds = 0
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Dangerous builds = 0
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uncompute v1
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uncompute volvor
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undump dperatom
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undump dlocal
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#
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# TEST 2:
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#
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# This compute voronoi generates
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# local and global quantities, but
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# not per-atom quantities
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compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
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# write voronoi local quantities to a file
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dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
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# sum up a voronoi local quantity
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compute sumarea all reduce sum c_v2[3]
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# output voronoi global quantities
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thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
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thermo 1
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run 0
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WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 8.787 | 8.787 | 8.787 Mbytes
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c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
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1215.0706 0 186 12 36 0
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Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms
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139.8% 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 | | 7.153e-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 = 10.1562
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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@ -1,170 +0,0 @@
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LAMMPS (27 Nov 2018)
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|
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using 1 OpenMP thread(s) per MPI task
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|
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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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|
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|
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dimension 2
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units metal
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|
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boundary f f p
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|
||||||
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|
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lattice hex 1.0 origin 0.25 0.25 0.0
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Lattice spacing in x,y,z = 1 1.73205 1
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atom_style atomic
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region box block 0 ${len} 0 ${len} 0.0 ${lenz}
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region box block 0 4 0 ${len} 0.0 ${lenz}
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region box block 0 4 0 4 0.0 ${lenz}
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region box block 0 4 0 4 0.0 10
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region atoms block 0 ${len} 0 ${len} 0.0 0.0
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region atoms block 0 4 0 ${len} 0.0 0.0
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region atoms block 0 4 0 4 0.0 0.0
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create_box 1 box
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Created orthogonal box = (0 0 0) to (4 6.9282 10)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 region atoms
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Created 32 atoms
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Time spent = 0.000311136 secs
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mass 1 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 0.0 1.0
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neighbor 1.0 nsq
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#
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# TEST 1:
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#
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||||||
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||||||
# This compute voronoi generates all three
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|
||||||
# types of quantity: per-atom, local, and global
|
|
||||||
|
|
||||||
compute v1 all voronoi/atom neighbors yes edge_histo 6
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|
||||||
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|
||||||
# write voronoi per-atom quantities to a file
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|
||||||
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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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|
||||||
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|
||||||
# writing voronoi local quantities to a file
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|
||||||
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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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|
||||||
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|
||||||
# sum up a voronoi per-atom quantity
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|
||||||
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|
||||||
compute volvor all reduce sum c_v1[1]
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|
||||||
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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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|
||||||
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||||||
# output voronoi global quantities
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||||||
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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]
|
|
||||||
thermo 1
|
|
||||||
|
|
||||||
run 0
|
|
||||||
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
|
||||||
Neighbor list info ...
|
|
||||||
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
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/cut, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/nsq/newton
|
|
||||||
stencil: none
|
|
||||||
bin: none
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 9.922 | 9.922 | 9.922 Mbytes
|
|
||||||
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
|
||||||
277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0
|
|
||||||
Loop time of 1.40667e-05 on 4 procs for 0 steps with 32 atoms
|
|
||||||
|
|
||||||
46.2% CPU use with 4 MPI tasks x 1 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 | | 1.407e-05 | | |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 (src/verlet.cpp:55)
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 8.671 | 8.671 | 8.671 Mbytes
|
|
||||||
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
|
|
||||||
1215.0706 0 186 12 36 0
|
|
||||||
Loop time of 2.71797e-05 on 4 procs for 0 steps with 32 atoms
|
|
||||||
|
|
||||||
57.9% CPU use with 4 MPI tasks x 1 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 | | 2.718e-05 | | |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
|
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Test volume definitions for 2d and finite systems
|
# Test volume definitions for 2d and finite systems
|
||||||
|
|
||||||
@ -9,57 +10,58 @@ variable len equal 4.0
|
|||||||
variable lenz equal 10.0
|
variable lenz equal 10.0
|
||||||
|
|
||||||
dimension 2
|
dimension 2
|
||||||
units metal
|
units metal
|
||||||
boundary p p p
|
boundary p p p
|
||||||
|
|
||||||
#lattice sq 1.0 origin 0.5 0.5 0.0
|
#lattice sq 1.0 origin 0.5 0.5 0.0
|
||||||
lattice hex 1.0 origin 0.5 0.5 0.0
|
lattice hex 1.0 origin 0.5 0.5 0.0
|
||||||
Lattice spacing in x,y,z = 1 1.73205 1
|
Lattice spacing in x,y,z = 1 1.7320508 1
|
||||||
|
|
||||||
atom_style atomic
|
atom_style atomic
|
||||||
|
|
||||||
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
|
region box block 0 ${len} 0 ${len} -0.5 0.5
|
||||||
region box block 0 4 0 ${len} 0.0 ${lenz}
|
region box block 0 4 0 ${len} -0.5 0.5
|
||||||
region box block 0 4 0 4 0.0 ${lenz}
|
region box block 0 4 0 4 -0.5 0.5
|
||||||
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 ${len} 0 ${len} 0.0 0.0
|
||||||
region atoms block 0 4 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
|
region atoms block 0 4 0 4 0.0 0.0
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
Created orthogonal box = (0 0 0) to (4 6.9282 10)
|
Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
|
||||||
1 by 1 by 1 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
create_atoms 1 region atoms
|
create_atoms 1 region atoms
|
||||||
Created 32 atoms
|
Created 32 atoms
|
||||||
Time spent = 0.000315905 secs
|
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
mass 1 1.0
|
mass 1 1.0
|
||||||
|
|
||||||
pair_style lj/cut ${rcut}
|
pair_style lj/cut ${rcut}
|
||||||
pair_style lj/cut 10
|
pair_style lj/cut 10
|
||||||
pair_coeff 1 1 0.0 1.0
|
pair_coeff 1 1 0.0 1.0
|
||||||
|
|
||||||
neighbor ${rskin} nsq
|
neighbor ${rskin} nsq
|
||||||
neighbor 2 nsq
|
neighbor 2 nsq
|
||||||
|
|
||||||
# set the minimum communication cut-off
|
# set the minimum communication cut-off
|
||||||
comm_modify cutoff ${rcomm}
|
comm_modify cutoff ${rcomm}
|
||||||
comm_modify cutoff 20
|
comm_modify cutoff 20
|
||||||
|
|
||||||
compute v1 all voronoi/atom neighbors yes
|
compute v1 all voronoi/atom neighbors yes
|
||||||
compute volvor all reduce sum c_v1[1]
|
compute volvor all reduce sum c_v1[1]
|
||||||
variable volsys equal lz*lx*ly
|
variable volsys equal lz*lx*ly
|
||||||
variable err equal c_volvor-v_volsys
|
variable err equal c_volvor-v_volsys
|
||||||
thermo_style custom c_volvor v_volsys vol v_err
|
thermo_style custom c_volvor v_volsys vol v_err
|
||||||
thermo 1
|
thermo 1
|
||||||
|
|
||||||
#
|
#
|
||||||
# TEST 1: Volume check for 2d bulk system
|
# TEST 1: Volume check for 2d bulk system
|
||||||
#
|
#
|
||||||
|
|
||||||
run 0
|
run 0
|
||||||
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 12
|
master list distance cutoff = 12
|
||||||
ghost atom cutoff = 20
|
ghost atom cutoff = 20
|
||||||
@ -69,12 +71,12 @@ Neighbor list info ...
|
|||||||
pair build: half/nsq/newton
|
pair build: half/nsq/newton
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.007 | 3.007 | 3.007 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.008 | 3.008 | 3.008 Mbytes
|
||||||
c_volvor v_volsys Volume v_err
|
c_volvor v_volsys Volume v_err
|
||||||
277.12813 277.12813 27.712813 5.6843419e-14
|
27.712813 27.712813 27.712813 -3.5527137e-15
|
||||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms
|
Loop time of 6.33e-07 on 1 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
316.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
@ -84,13 +86,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Other | | 9.537e-07 | | |100.00
|
Other | | 6.33e-07 | | |100.00
|
||||||
|
|
||||||
Nlocal: 32 ave 32 max 32 min
|
Nlocal: 32 ave 32 max 32 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 2415 ave 2415 max 2415 min
|
Nghost: 2415 ave 2415 max 2415 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 8256 ave 8256 max 8256 min
|
Neighs: 8256 ave 8256 max 8256 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 8256
|
Total # of neighbors = 8256
|
||||||
@ -103,15 +105,17 @@ Dangerous builds = 0
|
|||||||
# add margins in x and y directions
|
# add margins in x and y directions
|
||||||
#
|
#
|
||||||
|
|
||||||
change_box all boundary f f p
|
change_box all boundary f f p
|
||||||
run 0
|
Changing box ...
|
||||||
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Per MPI rank memory allocation (min/avg/max) = 7.688 | 7.688 | 7.688 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 7.688 | 7.688 | 7.688 Mbytes
|
||||||
c_volvor v_volsys Volume v_err
|
c_volvor v_volsys Volume v_err
|
||||||
277.12813 277.12813 27.712813 3.4106051e-13
|
27.712813 27.712813 27.712813 3.5527137e-14
|
||||||
Loop time of 4.76837e-07 on 1 procs for 0 steps with 32 atoms
|
Loop time of 3.93e-07 on 1 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
254.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
@ -121,13 +125,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Other | | 4.768e-07 | | |100.00
|
Other | | 3.93e-07 | | |100.00
|
||||||
|
|
||||||
Nlocal: 32 ave 32 max 32 min
|
Nlocal: 32 ave 32 max 32 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 0 ave 0 max 0 min
|
Nghost: 0 ave 0 max 0 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 496 ave 496 max 496 min
|
Neighs: 496 ave 496 max 496 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 496
|
Total # of neighbors = 496
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (27 Nov 2018)
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Test volume definitions for 2d and finite systems
|
# Test volume definitions for 2d and finite systems
|
||||||
|
|
||||||
@ -9,57 +10,58 @@ variable len equal 4.0
|
|||||||
variable lenz equal 10.0
|
variable lenz equal 10.0
|
||||||
|
|
||||||
dimension 2
|
dimension 2
|
||||||
units metal
|
units metal
|
||||||
boundary p p p
|
boundary p p p
|
||||||
|
|
||||||
#lattice sq 1.0 origin 0.5 0.5 0.0
|
#lattice sq 1.0 origin 0.5 0.5 0.0
|
||||||
lattice hex 1.0 origin 0.5 0.5 0.0
|
lattice hex 1.0 origin 0.5 0.5 0.0
|
||||||
Lattice spacing in x,y,z = 1 1.73205 1
|
Lattice spacing in x,y,z = 1 1.7320508 1
|
||||||
|
|
||||||
atom_style atomic
|
atom_style atomic
|
||||||
|
|
||||||
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
|
region box block 0 ${len} 0 ${len} -0.5 0.5
|
||||||
region box block 0 4 0 ${len} 0.0 ${lenz}
|
region box block 0 4 0 ${len} -0.5 0.5
|
||||||
region box block 0 4 0 4 0.0 ${lenz}
|
region box block 0 4 0 4 -0.5 0.5
|
||||||
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 ${len} 0 ${len} 0.0 0.0
|
||||||
region atoms block 0 4 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
|
region atoms block 0 4 0 4 0.0 0.0
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
Created orthogonal box = (0 0 0) to (4 6.9282 10)
|
Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
|
||||||
2 by 2 by 1 MPI processor grid
|
2 by 2 by 1 MPI processor grid
|
||||||
create_atoms 1 region atoms
|
create_atoms 1 region atoms
|
||||||
Created 32 atoms
|
Created 32 atoms
|
||||||
Time spent = 0.000319481 secs
|
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
mass 1 1.0
|
mass 1 1.0
|
||||||
|
|
||||||
pair_style lj/cut ${rcut}
|
pair_style lj/cut ${rcut}
|
||||||
pair_style lj/cut 10
|
pair_style lj/cut 10
|
||||||
pair_coeff 1 1 0.0 1.0
|
pair_coeff 1 1 0.0 1.0
|
||||||
|
|
||||||
neighbor ${rskin} nsq
|
neighbor ${rskin} nsq
|
||||||
neighbor 2 nsq
|
neighbor 2 nsq
|
||||||
|
|
||||||
# set the minimum communication cut-off
|
# set the minimum communication cut-off
|
||||||
comm_modify cutoff ${rcomm}
|
comm_modify cutoff ${rcomm}
|
||||||
comm_modify cutoff 20
|
comm_modify cutoff 20
|
||||||
|
|
||||||
compute v1 all voronoi/atom neighbors yes
|
compute v1 all voronoi/atom neighbors yes
|
||||||
compute volvor all reduce sum c_v1[1]
|
compute volvor all reduce sum c_v1[1]
|
||||||
variable volsys equal lz*lx*ly
|
variable volsys equal lz*lx*ly
|
||||||
variable err equal c_volvor-v_volsys
|
variable err equal c_volvor-v_volsys
|
||||||
thermo_style custom c_volvor v_volsys vol v_err
|
thermo_style custom c_volvor v_volsys vol v_err
|
||||||
thermo 1
|
thermo 1
|
||||||
|
|
||||||
#
|
#
|
||||||
# TEST 1: Volume check for 2d bulk system
|
# TEST 1: Volume check for 2d bulk system
|
||||||
#
|
#
|
||||||
|
|
||||||
run 0
|
run 0
|
||||||
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 12
|
master list distance cutoff = 12
|
||||||
ghost atom cutoff = 20
|
ghost atom cutoff = 20
|
||||||
@ -69,12 +71,12 @@ Neighbor list info ...
|
|||||||
pair build: half/nsq/newton
|
pair build: half/nsq/newton
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.042 | 3.042 | 3.042 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.038 | 3.038 | 3.038 Mbytes
|
||||||
c_volvor v_volsys Volume v_err
|
c_volvor v_volsys Volume v_err
|
||||||
277.12813 277.12813 27.712813 5.1159077e-13
|
27.712813 27.712813 27.712813 2.1316282e-14
|
||||||
Loop time of 2.79546e-05 on 4 procs for 0 steps with 32 atoms
|
Loop time of 2.18725e-06 on 4 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
51.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
45.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
@ -84,13 +86,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Other | | 2.795e-05 | | |100.00
|
Other | | 2.187e-06 | | |100.00
|
||||||
|
|
||||||
Nlocal: 8 ave 8 max 8 min
|
Nlocal: 8 ave 8 max 8 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 2159 ave 2159 max 2159 min
|
Nghost: 2159 ave 2159 max 2159 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 2064 ave 2077 max 2051 min
|
Neighs: 2064 ave 2077 max 2051 min
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
|
||||||
Total # of neighbors = 8256
|
Total # of neighbors = 8256
|
||||||
@ -103,15 +105,17 @@ Dangerous builds = 0
|
|||||||
# add margins in x and y directions
|
# add margins in x and y directions
|
||||||
#
|
#
|
||||||
|
|
||||||
change_box all boundary f f p
|
change_box all boundary f f p
|
||||||
run 0
|
Changing box ...
|
||||||
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
run 0
|
||||||
Per MPI rank memory allocation (min/avg/max) = 7.678 | 7.678 | 7.678 Mbytes
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
c_volvor v_volsys Volume v_err
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
277.12813 277.12813 27.712813 3.4106051e-13
|
Per MPI rank memory allocation (min/avg/max) = 7.671 | 7.671 | 7.671 Mbytes
|
||||||
Loop time of 1.88947e-05 on 4 procs for 0 steps with 32 atoms
|
c_volvor v_volsys Volume v_err
|
||||||
|
27.712813 27.712813 27.712813 3.907985e-14
|
||||||
|
Loop time of 2.22e-06 on 4 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
47.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
112.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
@ -121,13 +125,13 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Other | | 1.889e-05 | | |100.00
|
Other | | 2.22e-06 | | |100.00
|
||||||
|
|
||||||
Nlocal: 8 ave 8 max 8 min
|
Nlocal: 8 ave 8 max 8 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 24 ave 24 max 24 min
|
Nghost: 24 ave 24 max 24 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 124 ave 124 max 124 min
|
Neighs: 124 ave 124 max 124 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 496
|
Total # of neighbors = 496
|
||||||
168
examples/voronoi/log.6Dec23.voronoi.data.g++.1
Normal file
168
examples/voronoi/log.6Dec23.voronoi.data.g++.1
Normal file
@ -0,0 +1,168 @@
|
|||||||
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 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 1.7320508 1
|
||||||
|
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
region box block 0 ${len} 0 ${len} -0.5 0.5
|
||||||
|
region box block 0 4 0 ${len} -0.5 0.5
|
||||||
|
region box block 0 4 0 4 -0.5 0.5
|
||||||
|
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 -0.5) to (4 6.9282032 0.5)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 region atoms
|
||||||
|
Created 32 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
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 with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.5
|
||||||
|
ghost atom cutoff = 3.5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/nsq/newton
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes
|
||||||
|
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||||
|
27.712813 27.712813 27.712813 3.1974423e-14 0 186 12 36 0
|
||||||
|
Loop time of 7.96e-07 on 1 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
|
125.6% CPU use with 1 MPI tasks x 1 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 | | 7.96e-07 | | |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 = 10.15625
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
uncompute v1
|
||||||
|
uncompute volvor
|
||||||
|
undump dperatom
|
||||||
|
undump dlocal
|
||||||
|
|
||||||
|
#
|
||||||
|
# TEST 2:
|
||||||
|
#
|
||||||
|
|
||||||
|
# This compute voronoi generates peratom and local and global quantities
|
||||||
|
|
||||||
|
compute v2 all voronoi/atom neighbors yes edge_histo 6
|
||||||
|
|
||||||
|
# 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] inputs local
|
||||||
|
|
||||||
|
# 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 with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes
|
||||||
|
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
|
||||||
|
171.39013 0 186 12 36 0
|
||||||
|
Loop time of 3.74e-07 on 1 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 1 MPI tasks x 1 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 | | 3.74e-07 | | |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 = 10.15625
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
168
examples/voronoi/log.6Dec23.voronoi.data.g++.4
Normal file
168
examples/voronoi/log.6Dec23.voronoi.data.g++.4
Normal file
@ -0,0 +1,168 @@
|
|||||||
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 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 1.7320508 1
|
||||||
|
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
region box block 0 ${len} 0 ${len} -0.5 0.5
|
||||||
|
region box block 0 4 0 ${len} -0.5 0.5
|
||||||
|
region box block 0 4 0 4 -0.5 0.5
|
||||||
|
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 -0.5) to (4 6.9282032 0.5)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 region atoms
|
||||||
|
Created 32 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
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 with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.5
|
||||||
|
ghost atom cutoff = 3.5
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/nsq/newton
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes
|
||||||
|
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||||||
|
27.712813 27.712813 27.712813 3.907985e-14 0 186 12 36 0
|
||||||
|
Loop time of 2.21425e-06 on 4 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
|
45.2% CPU use with 4 MPI tasks x 1 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 | | 2.214e-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 = 10.15625
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
uncompute v1
|
||||||
|
uncompute volvor
|
||||||
|
undump dperatom
|
||||||
|
undump dlocal
|
||||||
|
|
||||||
|
#
|
||||||
|
# TEST 2:
|
||||||
|
#
|
||||||
|
|
||||||
|
# This compute voronoi generates peratom and local and global quantities
|
||||||
|
|
||||||
|
compute v2 all voronoi/atom neighbors yes edge_histo 6
|
||||||
|
|
||||||
|
# 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] inputs local
|
||||||
|
|
||||||
|
# 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 with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes
|
||||||
|
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
|
||||||
|
171.39013 0 186 12 36 0
|
||||||
|
Loop time of 1.82375e-06 on 4 procs for 0 steps with 32 atoms
|
||||||
|
|
||||||
|
82.2% CPU use with 4 MPI tasks x 1 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 | | 1.824e-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 = 10.15625
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user