forked from lijiext/lammps
634 lines
24 KiB
Groff
634 lines
24 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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 2 by 2 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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Time spent = 0.000644922 secs
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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 (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 = 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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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/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes
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c_r0
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1000
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Loop time of 2.08616e-06 on 4 procs for 0 steps with 4000 atoms
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167.8% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 2.086e-06 | | |100.00
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 17000 ave 17000 max 17000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 100000 ave 100000 max 100000 min
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Histogram: 4 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 (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes
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c_r0 c_r1
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1000 0
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Loop time of 4.52995e-06 on 4 procs for 0 steps with 4000 atoms
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132.5% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 4.53e-06 | | |100.00
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 17000 ave 17000 max 17000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 100000 ave 100000 max 100000 min
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Histogram: 4 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 (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes
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c_r0
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1000
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Loop time of 1.84774e-06 on 4 procs for 0 steps with 4000 atoms
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162.4% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 1.848e-06 | | |100.00
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 17000 ave 17000 max 17000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 100000 ave 100000 max 100000 min
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Histogram: 4 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 (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 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 0.181586 on 4 procs for 1 steps with 4000 atoms
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Performance: 0.476 ns/day, 50.441 hours/ns, 5.507 timesteps/s
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98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0015094 | 0.0015393 | 0.0016015 | 0.1 | 0.85
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00039601 | 0.00046033 | 0.00049233 | 0.0 | 0.25
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Output | 0.17947 | 0.1795 | 0.17956 | 0.0 | 98.85
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Modify | 4.7684e-07 | 7.1526e-07 | 9.5367e-07 | 0.0 | 0.00
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Other | | 9e-05 | | | 0.05
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 17000 ave 17000 max 17000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 100000 ave 100000 max 100000 min
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Histogram: 4 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 (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 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 0.184754 on 4 procs for 1 steps with 4000 atoms
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Performance: 0.468 ns/day, 51.321 hours/ns, 5.413 timesteps/s
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96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0015123 | 0.0015253 | 0.0015385 | 0.0 | 0.83
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00038028 | 0.00039649 | 0.00040984 | 0.0 | 0.21
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Output | 0.18271 | 0.18273 | 0.1828 | 0.0 | 98.91
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Modify | 7.1526e-07 | 8.9407e-07 | 9.5367e-07 | 0.0 | 0.00
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Other | | 0.0001001 | | | 0.05
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 17000 ave 17000 max 17000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 100000 ave 100000 max 100000 min
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Histogram: 4 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 (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 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 0.191424 on 4 procs for 1 steps with 4000 atoms
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Performance: 0.451 ns/day, 53.173 hours/ns, 5.224 timesteps/s
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98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0016205 | 0.0016853 | 0.0018284 | 0.2 | 0.88
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00041676 | 0.00055587 | 0.00062323 | 0.0 | 0.29
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Output | 0.18905 | 0.18907 | 0.18915 | 0.0 | 98.77
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Modify | 1.1921e-06 | 1.2517e-06 | 1.4305e-06 | 0.0 | 0.00
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Other | | 0.0001094 | | | 0.06
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 17000 ave 17000 max 17000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 100000 ave 100016 max 99984 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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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
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create_atoms 1 box
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Created 2000 atoms
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Time spent = 0.000178576 secs
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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 (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 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 16000 0
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0 0 0 12000 0 16000 0
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Loop time of 0.0871635 on 4 procs for 1 steps with 2000 atoms
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Performance: 0.991 ns/day, 24.212 hours/ns, 11.473 timesteps/s
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96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00038028 | 0.00038761 | 0.00040364 | 0.0 | 0.44
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00020146 | 0.00021631 | 0.00022292 | 0.0 | 0.25
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Output | 0.086468 | 0.086487 | 0.086541 | 0.0 | 99.22
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Modify | 4.7684e-07 | 7.1526e-07 | 9.5367e-07 | 0.0 | 0.00
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Other | | 7.224e-05 | | | 0.08
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Nlocal: 500 ave 500 max 500 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 8500 ave 8500 max 8500 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 28000 ave 28000 max 28000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 112000
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Ave neighs/atom = 56
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Neighbor list builds = 0
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Dangerous builds = 0
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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
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print "TEST_4d $(round(v_t4d))% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)"
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TEST_4d 0% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)
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uncompute v1
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# restore fcc lattice
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delete_atoms group all
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Deleted 2000 atoms, new total = 0
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lattice fcc 1 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 1 1 1
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create_atoms 1 box basis 1 2
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Created 4000 atoms
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Time spent = 0.000248909 secs
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#
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# TEST 5: Occupation analysis
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#
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print "START5"
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START5
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# start with pristine lattice
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variable i1 equal 13
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variable i2 equal 257
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compute v1 all voronoi/atom occupation
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compute r0 all reduce sum c_v1[1]
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compute r1 all reduce sum c_v1[2]
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variable d5a equal c_v1[${i1}][1]
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variable d5a equal c_v1[13][1]
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variable d5b equal c_v1[${i2}][1]
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variable d5b equal c_v1[257][1]
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variable d5c equal c_v1[${i1}][2]
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variable d5c equal c_v1[13][2]
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variable d5d equal c_v1[${i2}][2]
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variable d5d equal c_v1[257][2]
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thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
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run 0
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WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
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Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes
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c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
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4000 4000 1 1 1 1
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Loop time of 1.84774e-06 on 4 procs for 0 steps with 4000 atoms
|
|
|
|
189.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
Other | | 1.848e-06 | | |100.00
|
|
|
|
Nlocal: 1000 ave 1000 max 1000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 17000 ave 17000 max 17000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 100000 ave 100000 max 100000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 400000
|
|
Ave neighs/atom = 100
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
# expect 1 1 1 1 (one atom per cell each)
|
|
variable t5a equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
|
variable t5a equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
|
variable t5a equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
|
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
|
|
variable t5a equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
|
|
|
|
# move atom i1 next to atom i2
|
|
variable oxd equal x[${i1}]
|
|
variable oxd equal x[13]
|
|
variable oyd equal y[${i1}]
|
|
variable oyd equal y[13]
|
|
variable ozd equal z[${i1}]
|
|
variable ozd equal z[13]
|
|
# we need to freeze this value
|
|
variable ox equal ${oxd}
|
|
variable ox equal 3.25
|
|
variable oy equal ${oyd}
|
|
variable oy equal 0.25
|
|
variable oz equal ${ozd}
|
|
variable oz equal 0.25
|
|
# these coords dont change so dynamic evaluation is ok
|
|
variable nx equal x[${i2}]
|
|
variable nx equal x[257]
|
|
variable ny equal y[${i2}]
|
|
variable ny equal y[257]
|
|
variable nz equal z[${i2}]
|
|
variable nz equal z[257]
|
|
set atom ${i1} x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
|
|
set atom 13 x $(v_nx+0.2) y $(v_ny+0.2) z $(v_nz+0.2)
|
|
set atom 13 x 4.4500000000000001776 y $(v_ny+0.2) z $(v_nz+0.2)
|
|
set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z $(v_nz+0.2)
|
|
set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z 1.4499999999999999556
|
|
1 settings made for x
|
|
1 settings made for y
|
|
1 settings made for z
|
|
|
|
run 0
|
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
|
Per MPI rank memory allocation (min/avg/max) = 7.675 | 7.675 | 7.675 Mbytes
|
|
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
|
4000 4002 0 2 2 2
|
|
Loop time of 1.72853e-06 on 4 procs for 0 steps with 4000 atoms
|
|
|
|
188.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
Other | | 1.729e-06 | | |100.00
|
|
|
|
Nlocal: 1000 ave 1000 max 1000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 17000 ave 17000 max 17000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 99999.2 ave 100075 max 99967 min
|
|
Histogram: 2 1 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 399997
|
|
Ave neighs/atom = 99.9993
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
# expect 0 2 2 2 (vacancy at the original i1 site, interstitial at i2 and both atoms are now sharing a site)
|
|
variable t5b equal abs(${d5a}-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
|
variable t5b equal abs(0-0)+abs(${d5b}-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
|
variable t5b equal abs(0-0)+abs(2-2)+abs(${d5c}-2)+abs(${d5d}-2)
|
|
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(${d5d}-2)
|
|
variable t5b equal abs(0-0)+abs(2-2)+abs(2-2)+abs(2-2)
|
|
|
|
# move atom back
|
|
set atom ${i1} x ${ox} y ${oy} z ${oz}
|
|
set atom 13 x ${ox} y ${oy} z ${oz}
|
|
set atom 13 x 3.25 y ${oy} z ${oz}
|
|
set atom 13 x 3.25 y 0.25 z ${oz}
|
|
set atom 13 x 3.25 y 0.25 z 0.25
|
|
1 settings made for x
|
|
1 settings made for y
|
|
1 settings made for z
|
|
|
|
run 0
|
|
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
|
|
Per MPI rank memory allocation (min/avg/max) = 7.675 | 7.675 | 7.675 Mbytes
|
|
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
|
|
4000 4000 1 1 1 1
|
|
Loop time of 1.49012e-06 on 4 procs for 0 steps with 4000 atoms
|
|
|
|
218.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
Other | | 1.49e-06 | | |100.00
|
|
|
|
Nlocal: 1000 ave 1000 max 1000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 17000 ave 17000 max 17000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 100000 ave 100000 max 100000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 400000
|
|
Ave neighs/atom = 100
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
# expect 1 1 1 1 (restored to the initial state)
|
|
variable t5c equal abs(${d5a}-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
|
variable t5c equal abs(1-1)+abs(${d5b}-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
|
variable t5c equal abs(1-1)+abs(1-1)+abs(${d5c}-1)+abs(${d5d}-1)
|
|
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(${d5d}-1)
|
|
variable t5c equal abs(1-1)+abs(1-1)+abs(1-1)+abs(1-1)
|
|
|
|
print "TEST_5 $((v_t5a+v_t5b+v_t5c)*100)% Error. Detection of vacancies and interstitials using the {occupation} keyword."
|
|
TEST_5 0% Error. Detection of vacancies and interstitials using the {occupation} keyword.
|
|
|
|
uncompute v1
|
|
uncompute r0
|
|
uncompute r1
|
|
|
|
#
|
|
# TEST 6: Sum of all voronoi cells is the triclinic simulation cell volume
|
|
#
|
|
|
|
# switch to triclinic box
|
|
change_box all triclinic
|
|
triclinic box = (0 0 0) to (10 10 10) with tilt (0 0 0)
|
|
change_box all xy final 5.0 remap units box
|
|
triclinic box = (0 0 0) to (10 10 10) with tilt (5 0 0)
|
|
|
|
compute v1 all voronoi/atom
|
|
dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
|
|
compute r0 all reduce sum c_v1[1]
|
|
thermo_style custom c_r0
|
|
variable t6 equal c_r0
|
|
run 0
|
|
WARNING: No fixes defined, atoms won't move (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 = 2.3
|
|
ghost atom cutoff = 5
|
|
binsize = 1.15, bins = 14 9 9
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton/tri
|
|
stencil: half/bin/3d/newton/tri
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 9.493 | 9.493 | 9.493 Mbytes
|
|
c_r0
|
|
1000
|
|
Loop time of 1.96695e-06 on 4 procs for 0 steps with 4000 atoms
|
|
|
|
165.2% 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 | | 1.967e-06 | | |100.00
|
|
|
|
Nlocal: 1000 ave 1000 max 1000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 17900 ave 17900 max 17900 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 108000 ave 108000 max 108000 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 432000
|
|
Ave neighs/atom = 108
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
print "TEST_6 $(round((v_t6-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume"
|
|
TEST_6 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: 0:00:02
|