LAMMPS (17 Jun 2013) # Test of Kawasaki Dynamics on LJ test system units metal #newton off boundary p p p lattice fcc 1 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 1 1 1 atom_style atomic atom_modify sort 0 0.0 region box block 0 10 0 10 0 10 create_box 2 box Created orthogonal box = (0 0 0) to (10 10 10) 1 by 2 by 2 MPI processor grid create_atoms 1 box basis 1 2 Created 4000 atoms mass 1 50 mass 2 50 pair_style lj/cut 2.0 pair_coeff 1 1 0.0 1.0 pair_coeff 1 2 0.0 1.0 pair_coeff 2 2 0.0 1.0 neighbor 0.3 bin neigh_modify delay 10 # set the cut-off to 2.5x the cutoff from the potential communicate single cutoff 5.0 # atom radii per type variable r atom (type==1)*0.1+(type==2)*0.3 # groups group type1 type 1 3000 atoms in group type1 group type2 type 2 1000 atoms in group type2 thermo 1 # reduce computes #compute r1 type1 reduce sum c_v1[1] #compute r2 type2 reduce sum c_v1[1] #compute v1 all voronoi/atom radius v_r # # TEST 1: Sum of all voronoi cells is the simulation cell volume # compute v1 all voronoi/atom dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t1 equal c_r0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 5.0468 Mbytes r0 1000 Loop time of 2.14577e-06 on 4 procs for 0 steps with 4000 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 0 (0) Outpt time (%) = 0 (0) Other time (%) = 2.14577e-06 (100) Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 17000 ave 17000 max 17000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 100000 ave 100000 max 100000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400000 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume" TEST_1 0% Error. Sum of all voronoi cells is the simulation cell volume uncompute v1 uncompute r0 undump d1 # # TEST 2: Sum of all only_group voronoi cells is the simulation cell volume # compute v1 type2 voronoi/atom only_group dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] compute r0 type2 reduce sum c_v1[1] compute r1 type1 reduce sum c_v1[1] thermo_style custom c_r0 c_r1 variable t2a equal c_r0 variable t2b equal c_r1 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 5.0468 Mbytes r0 r1 1000 0 Loop time of 2.98023e-06 on 4 procs for 0 steps with 4000 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 0 (0) Outpt time (%) = 0 (0) Other time (%) = 2.98023e-06 (100) Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 17000 ave 17000 max 17000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 100000 ave 100000 max 100000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400000 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume" TEST_2a 0% Error. Sum of all only_group voronoi cells is the simulation cell volume print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero" TEST_2b 0% Error. Sum of all only_group not included voronoi cells is zero uncompute v1 uncompute r0 uncompute r1 undump d1 # # TEST 3: Sum of all radius voronoi cells is the simulation cell volume # compute v1 all voronoi/atom radius v_r dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t3 equal c_r0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 5.0468 Mbytes r0 1000 Loop time of 2.14577e-06 on 4 procs for 0 steps with 4000 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 0 (0) Outpt time (%) = 0 (0) Other time (%) = 2.14577e-06 (100) Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 17000 ave 17000 max 17000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 100000 ave 100000 max 100000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400000 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume" TEST_3 0% Error. Sum of all radius voronoi cells is the simulation cell volume uncompute v1 uncompute r0 undump d1 # # TEST 4: Edge histogram tests # compute v1 type2 voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 4.38301 Mbytes v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7] 0 0 0 12000 0 0 0 0 0 0 12000 0 0 0 Loop time of 0.442006 on 4 procs for 1 steps with 4000 atoms Pair time (%) = 0.00181943 (0.411631) Neigh time (%) = 0 (0) Comm time (%) = 0.000676751 (0.153109) Outpt time (%) = 0.439412 (99.4132) Other time (%) = 9.7394e-05 (0.0220345) Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 17000 ave 17000 max 17000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 100000 ave 100000 max 100000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400000 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120 print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)" TEST_4a 0% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side) uncompute v1 compute v1 all voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 4.38301 Mbytes v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7] 0 0 0 48000 0 0 0 0 0 0 48000 0 0 0 Loop time of 0.423468 on 4 procs for 1 steps with 4000 atoms Pair time (%) = 0.00182724 (0.431494) Neigh time (%) = 0 (0) Comm time (%) = 0.000680804 (0.160769) Outpt time (%) = 0.420859 (99.3838) Other time (%) = 0.000101268 (0.023914) Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 17000 ave 17000 max 17000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 100000 ave 100000 max 100000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400000 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 variable t4b equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480 print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)" TEST_4b 0% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side) uncompute v1 # perturbed fcc lattice displace_atoms all random 0.01 0.01 0.01 31423 compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 4.38301 Mbytes v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7] 0 0 0 48000 0 0 0 0 0 0 48000 0 0 0 Loop time of 0.450853 on 4 procs for 1 steps with 4000 atoms Pair time (%) = 0.00191522 (0.424798) Neigh time (%) = 0 (0) Comm time (%) = 0.000696659 (0.15452) Outpt time (%) = 0.448143 (99.3988) Other time (%) = 9.85861e-05 (0.0218666) Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 17000 ave 17000 max 17000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 100000 ave 100016 max 99984 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 400000 Ave neighs/atom = 100 Neighbor list builds = 0 Dangerous builds = 0 variable t4c equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480 print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold" TEST_4c 0% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold uncompute v1 # bcc lattice delete_atoms group all Deleted 4000 atoms, new total = 0 lattice bcc 1 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 1 1 1 create_atoms 1 box Created 2000 atoms compute v1 all voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 4.38301 Mbytes v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7] 0 0 0 12000 0 16000 0 0 0 0 12000 0 16000 0 Loop time of 0.206755 on 4 procs for 1 steps with 2000 atoms Pair time (%) = 0.000465989 (0.225382) Neigh time (%) = 0 (0) Comm time (%) = 0.000327706 (0.1585) Outpt time (%) = 0.205902 (99.5874) Other time (%) = 5.94258e-05 (0.0287421) Nlocal: 500 ave 500 max 500 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 8500 ave 8500 max 8500 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 28000 ave 28000 max 28000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112000 Ave neighs/atom = 56 Neighbor list builds = 0 Dangerous builds = 0 variable t4d equal (abs(c_v1[4]-12000)+abs(c_v1[6]-16000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[7])/280 print "TEST_4d $(round(v_t4d))% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges)" TEST_4d 0% Error. Edge histogram of a body centered cubic lattice (truncated octahedron, 6 sides with 4 edges, 8 sides with 6 edges) uncompute v1 # restore fcc lattice delete_atoms group all Deleted 2000 atoms, new total = 0 lattice fcc 1 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 1 1 1 create_atoms 1 box basis 1 2 Created 4000 atoms # # TEST 5: 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 t5 equal c_r0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) Memory usage per processor = 5.2072 Mbytes r0 1000 Loop time of 2.38419e-06 on 4 procs for 0 steps with 4000 atoms Pair time (%) = 0 (0) Neigh time (%) = 0 (0) Comm time (%) = 0 (0) Outpt time (%) = 0 (0) Other time (%) = 2.38419e-06 (100) 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_5 $(round((v_t5-1000)/10))% Error. Sum of all voronoi cells is the triclinic simulation cell volume" TEST_5 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