Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/examples/voronoi/log.voronoi.4Aug13.macos.4
666de878addclammm-master-deprecated

Last Change
Raw File

log.voronoi.4Aug13.macos.4
View Options

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
c4science · Help