forked from lijiext/lammps
620 lines
23 KiB
Groff
620 lines
23 KiB
Groff
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LAMMPS (5 Oct 2016)
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# Test of Kawasaki Dynamics on LJ test system
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units metal
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#newton off
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boundary p p p
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lattice fcc 1 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 1 1 1
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atom_style atomic
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# indexed atom variables in test 5 need a map
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atom_modify sort 0 0.0 map hash
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region box block 0 10 0 10 0 10
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create_box 2 box
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Created orthogonal box = (0 0 0) to (10 10 10)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box basis 1 2
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Created 4000 atoms
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mass 1 50
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mass 2 50
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pair_style lj/cut 2.0
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pair_coeff 1 1 0.0 1.0
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pair_coeff 1 2 0.0 1.0
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pair_coeff 2 2 0.0 1.0
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neighbor 0.3 bin
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neigh_modify delay 10
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# set the cut-off to 2.5x the cutoff from the potential
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comm_modify cutoff 5.0
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# atom radii per type
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variable r atom (type==1)*0.1+(type==2)*0.3
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# groups
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group type1 type 1
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3000 atoms in group type1
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group type2 type 2
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1000 atoms in group type2
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thermo 1
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# reduce computes
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#compute r1 type1 reduce sum c_v1[1]
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#compute r2 type2 reduce sum c_v1[1]
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#compute v1 all voronoi/atom radius v_r
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#
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# TEST 1: Sum of all voronoi cells is the simulation cell volume
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#
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compute v1 all voronoi/atom
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dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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compute r0 all reduce sum c_v1[1]
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thermo_style custom c_r0
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variable t1 equal c_r0
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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 = 2.3
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ghost atom cutoff = 5
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binsize = 1.15 -> bins = 9 9 9
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Memory usage per processor = 8.74398 Mbytes
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c_r0
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1000
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Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 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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---------------------------------------------------------------
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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 | | 9.537e-07 | | |100.00
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 28000 ave 28000 max 28000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 400000 ave 400000 max 400000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 400000
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Ave neighs/atom = 100
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Neighbor list builds = 0
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Dangerous builds = 0
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print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume"
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TEST_1 0% Error. Sum of all voronoi cells is the simulation cell volume
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uncompute v1
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uncompute r0
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undump d1
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#
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# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume
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#
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compute v1 type2 voronoi/atom only_group
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dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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compute r0 type2 reduce sum c_v1[1]
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compute r1 type1 reduce sum c_v1[1]
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thermo_style custom c_r0 c_r1
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variable t2a equal c_r0
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variable t2b equal c_r1
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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 = 8.74398 Mbytes
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c_r0 c_r1
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1000 0
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Loop time of 0 on 1 procs for 0 steps with 4000 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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---------------------------------------------------------------
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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: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 28000 ave 28000 max 28000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 400000 ave 400000 max 400000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 400000
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Ave neighs/atom = 100
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Neighbor list builds = 0
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Dangerous builds = 0
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print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume"
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TEST_2a 0% Error. Sum of all only_group voronoi cells is the simulation cell volume
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print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero"
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TEST_2b 0% Error. Sum of all only_group not included voronoi cells is zero
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uncompute v1
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uncompute r0
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uncompute r1
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undump d1
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#
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# TEST 3: Sum of all radius voronoi cells is the simulation cell volume
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#
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compute v1 all voronoi/atom radius v_r
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dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
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compute r0 all reduce sum c_v1[1]
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thermo_style custom c_r0
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variable t3 equal c_r0
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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 = 8.74398 Mbytes
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c_r0
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1000
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Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 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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---------------------------------------------------------------
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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 | | 9.537e-07 | | |100.00
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 28000 ave 28000 max 28000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 400000 ave 400000 max 400000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 400000
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Ave neighs/atom = 100
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Neighbor list builds = 0
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Dangerous builds = 0
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print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume"
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TEST_3 0% Error. Sum of all radius voronoi cells is the simulation cell volume
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uncompute v1
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uncompute r0
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undump d1
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#
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# TEST 4: Edge histogram tests
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#
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compute v1 type2 voronoi/atom edge_histo 8
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thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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run 1
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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Memory usage per processor = 6.53036 Mbytes
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c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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0 0 0 12000 0 0 0
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0 0 0 12000 0 0 0
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Loop time of 0.454686 on 1 procs for 1 steps with 4000 atoms
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Performance: 0.190 ns/day, 126.302 hours/ns, 2.199 timesteps/s
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99.8% 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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---------------------------------------------------------------
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Pair | 0.0058758 | 0.0058758 | 0.0058758 | 0.0 | 1.29
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0001812 | 0.0001812 | 0.0001812 | 0.0 | 0.04
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Output | 0.44856 | 0.44856 | 0.44856 | 0.0 | 98.65
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Modify | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 0.00
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Other | | 6.723e-05 | | | 0.01
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 28000 ave 28000 max 28000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 400000 ave 400000 max 400000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 400000
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Ave neighs/atom = 100
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Neighbor list builds = 0
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Dangerous builds = 0
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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
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print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)"
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TEST_4a 0% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)
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uncompute v1
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compute v1 all voronoi/atom edge_histo 8
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thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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run 1
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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Memory usage per processor = 6.53036 Mbytes
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c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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0 0 0 48000 0 0 0
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0 0 0 48000 0 0 0
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Loop time of 0.474271 on 1 procs for 1 steps with 4000 atoms
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Performance: 0.182 ns/day, 131.742 hours/ns, 2.108 timesteps/s
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100.1% 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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---------------------------------------------------------------
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Pair | 0.005832 | 0.005832 | 0.005832 | 0.0 | 1.23
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00016904 | 0.00016904 | 0.00016904 | 0.0 | 0.04
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Output | 0.46822 | 0.46822 | 0.46822 | 0.0 | 98.72
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 5.007e-05 | | | 0.01
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 28000 ave 28000 max 28000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 400000 ave 400000 max 400000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 400000
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Ave neighs/atom = 100
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Neighbor list builds = 0
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Dangerous builds = 0
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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
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print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)"
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TEST_4b 0% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)
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uncompute v1
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# perturbed fcc lattice
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displace_atoms all random 0.01 0.01 0.01 31423
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compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1
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thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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run 1
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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Memory usage per processor = 6.53036 Mbytes
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c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
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0 0 0 48000 0 0 0
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0 0 0 48000 0 0 0
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Loop time of 0.465207 on 1 procs for 1 steps with 4000 atoms
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Performance: 0.186 ns/day, 129.224 hours/ns, 2.150 timesteps/s
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99.7% 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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---------------------------------------------------------------
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Pair | 0.006129 | 0.006129 | 0.006129 | 0.0 | 1.32
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00016928 | 0.00016928 | 0.00016928 | 0.0 | 0.04
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Output | 0.45886 | 0.45886 | 0.45886 | 0.0 | 98.64
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Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
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Other | | 4.482e-05 | | | 0.01
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 28000 ave 28000 max 28000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 400000 ave 400000 max 400000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 400000
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Ave neighs/atom = 100
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Neighbor list builds = 0
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Dangerous builds = 0
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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
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print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold"
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TEST_4c 0% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold
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uncompute v1
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# bcc lattice
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delete_atoms group all
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Deleted 4000 atoms, new total = 0
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lattice bcc 1 origin 0.25 0.25 0.25
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||
|
|
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 = 6.53036 Mbytes
|
||
|
|
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
|
||
|
|
0 0 0 12000 0 16000 0
|
||
|
|
0 0 0 12000 0 16000 0
|
||
|
|
Loop time of 0.196673 on 1 procs for 1 steps with 2000 atoms
|
||
|
|
|
||
|
|
Performance: 0.439 ns/day, 54.631 hours/ns, 5.085 timesteps/s
|
||
|
|
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0.0014789 | 0.0014789 | 0.0014789 | 0.0 | 0.75
|
||
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Comm | 8.1062e-05 | 8.1062e-05 | 8.1062e-05 | 0.0 | 0.04
|
||
|
|
Output | 0.19509 | 0.19509 | 0.19509 | 0.0 | 99.20
|
||
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Other | | 1.907e-05 | | | 0.01
|
||
|
|
|
||
|
|
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[${i2}][2]
|
||
|
|
variable d5d equal c_v1[257][2]
|
||
|
|
thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
||
|
|
|
||
|
|
run 0
|
||
|
|
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||
|
|
Memory usage per processor = 6.53036 Mbytes
|
||
|
|
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
||
|
|
4000 4000 1 1 1 1
|
||
|
|
Loop time of 0 on 1 procs for 0 steps with 4000 atoms
|
||
|
|
|
||
|
|
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Other | | 0 | | | 0.00
|
||
|
|
|
||
|
|
Nlocal: 4000 ave 4000 max 4000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Nghost: 28000 ave 28000 max 28000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Neighs: 400000 ave 400000 max 400000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 400000
|
||
|
|
Ave neighs/atom = 100
|
||
|
|
Neighbor list builds = 0
|
||
|
|
Dangerous builds = 0
|
||
|
|
# expect 1 1 1 1 (one atom per cell each)
|
||
|
|
variable t5a equal abs(${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 $(v_nz+0.2)
|
||
|
|
set atom 13 x 4.4500000000000001776 y 6.4500000000000001776 z 0.4500000000000000111
|
||
|
|
1 settings made for x
|
||
|
|
1 settings made for y
|
||
|
|
1 settings made for z
|
||
|
|
|
||
|
|
run 0
|
||
|
|
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||
|
|
Memory usage per processor = 7.03036 Mbytes
|
||
|
|
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
||
|
|
4000 4002 0 2 2 2
|
||
|
|
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
|
||
|
|
|
||
|
|
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Other | | 9.537e-07 | | |100.00
|
||
|
|
|
||
|
|
Nlocal: 4000 ave 4000 max 4000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Nghost: 28000 ave 28000 max 28000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Neighs: 399998 ave 399998 max 399998 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 399998
|
||
|
|
Ave neighs/atom = 99.9995
|
||
|
|
Neighbor list builds = 0
|
||
|
|
Dangerous builds = 0
|
||
|
|
# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
|
||
|
|
variable t5b equal abs(${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 ${oz}
|
||
|
|
set atom 13 x 3.25 y 0.25 z 0.25
|
||
|
|
1 settings made for x
|
||
|
|
1 settings made for y
|
||
|
|
1 settings made for z
|
||
|
|
|
||
|
|
run 0
|
||
|
|
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||
|
|
Memory usage per processor = 7.03036 Mbytes
|
||
|
|
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
||
|
|
4000 4000 1 1 1 1
|
||
|
|
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
|
||
|
|
|
||
|
|
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||
|
|
Other | | 9.537e-07 | | |100.00
|
||
|
|
|
||
|
|
Nlocal: 4000 ave 4000 max 4000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Nghost: 28000 ave 28000 max 28000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Neighs: 400000 ave 400000 max 400000 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 400000
|
||
|
|
Ave neighs/atom = 100
|
||
|
|
Neighbor list builds = 0
|
||
|
|
Dangerous builds = 0
|
||
|
|
# expect 1 1 1 1 (restored to the initial state)
|
||
|
|
variable t5c equal abs(${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 = 12.5794 Mbytes
|
||
|
|
c_r0
|
||
|
|
1000
|
||
|
|
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: 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: 0:00:06
|