From 137702f4712fed268f0d4b3e38c3dc658a29b02b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 29 Jul 2013 15:10:40 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10459 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/voronoi/in.voronoi | 3 +- examples/voronoi/log.voronoi.4Aug13.macos.1 | 368 ++++++++++++++++++++ examples/voronoi/log.voronoi.4Aug13.macos.4 | 368 ++++++++++++++++++++ 3 files changed, 737 insertions(+), 2 deletions(-) create mode 100644 examples/voronoi/log.voronoi.4Aug13.macos.1 create mode 100644 examples/voronoi/log.voronoi.4Aug13.macos.4 diff --git a/examples/voronoi/in.voronoi b/examples/voronoi/in.voronoi index 671a7c9b54..a9af704608 100644 --- a/examples/voronoi/in.voronoi +++ b/examples/voronoi/in.voronoi @@ -92,7 +92,7 @@ undump d1 # # TEST 4: Edge histogram tests # -compute v1 type2 voronoi/atom edge_histo 6 +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 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 @@ -150,6 +150,5 @@ uncompute v1 uncompute r0 undump d1 - # All tests done print TEST_DONE diff --git a/examples/voronoi/log.voronoi.4Aug13.macos.1 b/examples/voronoi/log.voronoi.4Aug13.macos.1 new file mode 100644 index 0000000000..cccaf3f603 --- /dev/null +++ b/examples/voronoi/log.voronoi.4Aug13.macos.1 @@ -0,0 +1,368 @@ +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 1 by 1 MPI processor grid +create_atoms 1 box basis 1 2 +Created 4000 atoms + +mass 1 50 +mass 2 50 + +pair_style lj/cut 2.0 +pair_coeff 1 1 0.0 1.0 +pair_coeff 1 2 0.0 1.0 +pair_coeff 2 2 0.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 10 + +# set the cut-off to 2.5x the cutoff from the potential +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 = 9.50465 Mbytes +r0 + 1000 +Loop time of 1.19209e-06 on 1 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 (%) = 1.19209e-06 (100) + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 28000 ave 28000 max 28000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 400000 ave 400000 max 400000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 400000 +Ave neighs/atom = 100 +Neighbor list builds = 0 +Dangerous builds = 0 +print "TEST_1 $(round(abs(v_t1-1000)/10))% Error. Sum of all voronoi cells is the simulation cell volume" +TEST_1 0% Error. Sum of all voronoi cells is the simulation cell volume +uncompute v1 +uncompute r0 +undump d1 + +# +# TEST 2: Sum of all only_group voronoi cells is the simulation cell volume +# +compute v1 type2 voronoi/atom only_group +dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] +compute r0 type2 reduce sum c_v1[1] +compute r1 type1 reduce sum c_v1[1] +thermo_style custom c_r0 c_r1 +variable t2a equal c_r0 +variable t2b equal c_r1 +run 0 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) +Memory usage per processor = 9.50465 Mbytes +r0 r1 + 1000 0 +Loop time of 0 on 1 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 (%) = 0 (0) + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 28000 ave 28000 max 28000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 400000 ave 400000 max 400000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 400000 +Ave neighs/atom = 100 +Neighbor list builds = 0 +Dangerous builds = 0 +print "TEST_2a $(round(abs(v_t2a-1000)/10))% Error. Sum of all only_group voronoi cells is the simulation cell volume" +TEST_2a 0% Error. Sum of all only_group voronoi cells is the simulation cell volume +print "TEST_2b $(round(v_t2b/10))% Error. Sum of all only_group not included voronoi cells is zero" +TEST_2b 0% Error. Sum of all only_group not included voronoi cells is zero +uncompute v1 +uncompute r0 +uncompute r1 +undump d1 + +# +# TEST 3: Sum of all radius voronoi cells is the simulation cell volume +# +compute v1 all voronoi/atom radius v_r +dump d1 all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] +compute r0 all reduce sum c_v1[1] +thermo_style custom c_r0 +variable t3 equal c_r0 +run 0 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) +Memory usage per processor = 9.50465 Mbytes +r0 + 1000 +Loop time of 9.53674e-07 on 1 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 (%) = 9.53674e-07 (100) + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 28000 ave 28000 max 28000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 400000 ave 400000 max 400000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 400000 +Ave neighs/atom = 100 +Neighbor list builds = 0 +Dangerous builds = 0 +print "TEST_3 $(round(abs(v_t3-1000)/10))% Error. Sum of all radius voronoi cells is the simulation cell volume" +TEST_3 0% Error. Sum of all radius voronoi cells is the simulation cell volume +uncompute v1 +uncompute r0 +undump d1 + + +# +# TEST 4: Edge histogram tests +# +compute v1 type2 voronoi/atom edge_histo 8 +thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +run 1 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) +Memory usage per processor = 8.07029 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 0.781288 on 1 procs for 1 steps with 4000 atoms + +Pair time (%) = 0.00799012 (1.02269) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000320911 (0.0410747) +Outpt time (%) = 0.772875 (98.9232) +Other time (%) = 0.000101805 (0.0130304) + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 28000 ave 28000 max 28000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 400000 ave 400000 max 400000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 400000 +Ave neighs/atom = 100 +Neighbor list builds = 0 +Dangerous builds = 0 +variable t4a equal (abs(c_v1[4]-12000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/120 +print "TEST_4a $(round(v_t4a))% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side)" +TEST_4a 0% Error. Edge histogram of a simple cubic lattice (6 sides. 4 edges per side) +uncompute v1 +compute v1 all voronoi/atom edge_histo 8 +thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +run 1 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) +Memory usage per processor = 8.07029 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 0.80266 on 1 procs for 1 steps with 4000 atoms + +Pair time (%) = 0.00799513 (0.996079) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000322819 (0.0402186) +Outpt time (%) = 0.794241 (98.9511) +Other time (%) = 0.000101089 (0.0125943) + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 28000 ave 28000 max 28000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 400000 ave 400000 max 400000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 400000 +Ave neighs/atom = 100 +Neighbor list builds = 0 +Dangerous builds = 0 +variable t4b equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480 +print "TEST_4b $(round(v_t4b))% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side)" +TEST_4b 0% Error. Edge histogram of a face centered cubic lattice (12 sides. 4 edges per side) +uncompute v1 + +# perturbed fcc lattice +displace_atoms all random 0.01 0.01 0.01 31423 +compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1 +thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +run 1 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) +Memory usage per processor = 8.07029 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 0.845146 on 1 procs for 1 steps with 4000 atoms + +Pair time (%) = 0.00830793 (0.983018) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000324011 (0.0383379) +Outpt time (%) = 0.836411 (98.9665) +Other time (%) = 0.000102997 (0.0121869) + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 28000 ave 28000 max 28000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 400000 ave 400000 max 400000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 400000 +Ave neighs/atom = 100 +Neighbor list builds = 0 +Dangerous builds = 0 +variable t4c equal (abs(c_v1[4]-48000)+c_v1[1]+c_v1[2]+c_v1[3]+c_v1[5]+c_v1[6]+c_v1[7])/480 +print "TEST_4c $(round(v_t4c))% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold" +TEST_4c 0% Error. Edge histogram of a perturbed face centered cubic lattice with edge_threshold +uncompute v1 + +# bcc lattice +delete_atoms group all +Deleted 4000 atoms, new total = 0 +lattice bcc 1 origin 0.25 0.25 0.25 +Lattice spacing in x,y,z = 1 1 1 +create_atoms 1 box +Created 2000 atoms +compute v1 all voronoi/atom edge_histo 8 +thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] +run 1 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:54) +Memory usage per processor = 8.07029 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 0.359532 on 1 procs for 1 steps with 2000 atoms + +Pair time (%) = 0.00208998 (0.581305) +Neigh time (%) = 0 (0) +Comm time (%) = 0.000163794 (0.0455574) +Outpt time (%) = 0.357227 (99.3589) +Other time (%) = 5.126e-05 (0.0142574) + +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: 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 = 9.9792 Mbytes +r0 + 1000 +Loop time of 9.53674e-07 on 1 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 (%) = 9.53674e-07 (100) + +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_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 diff --git a/examples/voronoi/log.voronoi.4Aug13.macos.4 b/examples/voronoi/log.voronoi.4Aug13.macos.4 new file mode 100644 index 0000000000..4c9460d3c7 --- /dev/null +++ b/examples/voronoi/log.voronoi.4Aug13.macos.4 @@ -0,0 +1,368 @@ +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