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make 2d system box center on 0.0

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This commit is contained in:
Axel Kohlmeyer
2023-12-06 07:36:29 -05:00
parent dd6b77d570
commit 58787ddecd
8 changed files with 465 additions and 461 deletions
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2
examples/voronoi/in.voronoi.2d
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@ -15,7 +15,7 @@ lattice hex 1.0 origin 0.5 0.5 0.0
atom_style atomic
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
region box block 0 ${len} 0 ${len} -0.5 0.5
region atoms block 0 ${len} 0 ${len} 0.0 0.0
create_box 1 box
create_atoms 1 region atoms

2
examples/voronoi/in.voronoi.data
View File

@ -11,7 +11,7 @@ lattice hex 1.0 origin 0.25 0.25 0.0
atom_style atomic
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
region box block 0 ${len} 0 ${len} -0.5 0.5
region atoms block 0 ${len} 0 ${len} 0.0 0.0
create_box 1 box
create_atoms 1 region atoms

170
examples/voronoi/log.27Nov18.voronoi.data.g++.1
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@ -1,170 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Exercise different output data options
variable len equal 4.0
variable lenz equal 10.0
dimension 2
units metal
boundary f f p
lattice hex 1.0 origin 0.25 0.25 0.0
Lattice spacing in x,y,z = 1 1.73205 1
atom_style atomic
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
region box block 0 4 0 ${len} 0.0 ${lenz}
region box block 0 4 0 4 0.0 ${lenz}
region box block 0 4 0 4 0.0 10
region atoms block 0 ${len} 0 ${len} 0.0 0.0
region atoms block 0 4 0 ${len} 0.0 0.0
region atoms block 0 4 0 4 0.0 0.0
create_box 1 box
Created orthogonal box = (0 0 0) to (4 6.9282 10)
1 by 1 by 1 MPI processor grid
create_atoms 1 region atoms
Created 32 atoms
Time spent = 0.000315666 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 0.0 1.0
neighbor 1.0 nsq
#
# TEST 1:
#
# This compute voronoi generates all three
# types of quantity: per-atom, local, and global
compute v1 all voronoi/atom neighbors yes edge_histo 6
# write voronoi per-atom quantities to a file
dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
# writing voronoi local quantities to a file
dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
# sum up a voronoi per-atom quantity
compute volvor all reduce sum c_v1[1]
variable volsys equal lz*lx*ly
variable err equal c_volvor-v_volsys
# output voronoi global quantities
thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
thermo 1
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 = 3.5
ghost atom cutoff = 3.5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/nsq/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.04 | 10.04 | 10.04 Mbytes
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0
Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms
0.0% CPU use with 1 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 | | 7.153e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 325 ave 325 max 325 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 325
Ave neighs/atom = 10.1562
Neighbor list builds = 0
Dangerous builds = 0
uncompute v1
uncompute volvor
undump dperatom
undump dlocal
#
# TEST 2:
#
# This compute voronoi generates
# local and global quantities, but
# not per-atom quantities
compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
# write voronoi local quantities to a file
dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
# sum up a voronoi local quantity
compute sumarea all reduce sum c_v2[3]
# output voronoi global quantities
thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
thermo 1
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 8.787 | 8.787 | 8.787 Mbytes
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
1215.0706 0 186 12 36 0
Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms
139.8% CPU use with 1 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 | | 7.153e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 325 ave 325 max 325 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 325
Ave neighs/atom = 10.1562
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

170
examples/voronoi/log.27Nov18.voronoi.data.g++.4
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@ -1,170 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Exercise different output data options
variable len equal 4.0
variable lenz equal 10.0
dimension 2
units metal
boundary f f p
lattice hex 1.0 origin 0.25 0.25 0.0
Lattice spacing in x,y,z = 1 1.73205 1
atom_style atomic
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
region box block 0 4 0 ${len} 0.0 ${lenz}
region box block 0 4 0 4 0.0 ${lenz}
region box block 0 4 0 4 0.0 10
region atoms block 0 ${len} 0 ${len} 0.0 0.0
region atoms block 0 4 0 ${len} 0.0 0.0
region atoms block 0 4 0 4 0.0 0.0
create_box 1 box
Created orthogonal box = (0 0 0) to (4 6.9282 10)
2 by 2 by 1 MPI processor grid
create_atoms 1 region atoms
Created 32 atoms
Time spent = 0.000311136 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 0.0 1.0
neighbor 1.0 nsq
#
# TEST 1:
#
# This compute voronoi generates all three
# types of quantity: per-atom, local, and global
compute v1 all voronoi/atom neighbors yes edge_histo 6
# write voronoi per-atom quantities to a file
dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
# writing voronoi local quantities to a file
dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
# sum up a voronoi per-atom quantity
compute volvor all reduce sum c_v1[1]
variable volsys equal lz*lx*ly
variable err equal c_volvor-v_volsys
# output voronoi global quantities
thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
thermo 1
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 = 3.5
ghost atom cutoff = 3.5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/nsq/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.922 | 9.922 | 9.922 Mbytes
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0
Loop time of 1.40667e-05 on 4 procs for 0 steps with 32 atoms
46.2% 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 | | 1.407e-05 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 24 ave 24 max 24 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 81.25 ave 84 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 325
Ave neighs/atom = 10.1562
Neighbor list builds = 0
Dangerous builds = 0
uncompute v1
uncompute volvor
undump dperatom
undump dlocal
#
# TEST 2:
#
# This compute voronoi generates
# local and global quantities, but
# not per-atom quantities
compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
# write voronoi local quantities to a file
dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
# sum up a voronoi local quantity
compute sumarea all reduce sum c_v2[3]
# output voronoi global quantities
thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
thermo 1
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 8.671 | 8.671 | 8.671 Mbytes
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
1215.0706 0 186 12 36 0
Loop time of 2.71797e-05 on 4 procs for 0 steps with 32 atoms
57.9% 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 | | 2.718e-05 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 24 ave 24 max 24 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 81.25 ave 84 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 325
Ave neighs/atom = 10.1562
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

44
examples/voronoi/log.27Nov18.voronoi.2d.g++.1 → examples/voronoi/log.6Dec23.voronoi.2d.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (27 Nov 2018)
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Test volume definitions for 2d and finite systems
@ -14,23 +15,23 @@ boundary p p p
#lattice sq 1.0 origin 0.5 0.5 0.0
lattice hex 1.0 origin 0.5 0.5 0.0
Lattice spacing in x,y,z = 1 1.73205 1
Lattice spacing in x,y,z = 1 1.7320508 1
atom_style atomic
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
region box block 0 4 0 ${len} 0.0 ${lenz}
region box block 0 4 0 4 0.0 ${lenz}
region box block 0 4 0 4 0.0 10
region box block 0 ${len} 0 ${len} -0.5 0.5
region box block 0 4 0 ${len} -0.5 0.5
region box block 0 4 0 4 -0.5 0.5
region atoms block 0 ${len} 0 ${len} 0.0 0.0
region atoms block 0 4 0 ${len} 0.0 0.0
region atoms block 0 4 0 4 0.0 0.0
create_box 1 box
Created orthogonal box = (0 0 0) to (4 6.9282 10)
Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
1 by 1 by 1 MPI processor grid
create_atoms 1 region atoms
Created 32 atoms
Time spent = 0.000315905 secs
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
create_atoms CPU = 0.000 seconds
mass 1 1.0
@ -57,9 +58,10 @@ thermo 1
#
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 20
@ -69,12 +71,12 @@ Neighbor list info ...
pair build: half/nsq/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.007 | 3.007 | 3.007 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.008 | 3.008 | 3.008 Mbytes
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 5.6843419e-14
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms
27.712813 27.712813 27.712813 -3.5527137e-15
Loop time of 6.33e-07 on 1 procs for 0 steps with 32 atoms
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
316.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -84,7 +86,7 @@ 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
Other | | 6.33e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -104,14 +106,16 @@ Dangerous builds = 0
#
change_box all boundary f f p
Changing box ...
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.688 | 7.688 | 7.688 Mbytes
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 3.4106051e-13
Loop time of 4.76837e-07 on 1 procs for 0 steps with 32 atoms
27.712813 27.712813 27.712813 3.5527137e-14
Loop time of 3.93e-07 on 1 procs for 0 steps with 32 atoms
209.7% CPU use with 1 MPI tasks x 1 OpenMP threads
254.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -121,7 +125,7 @@ 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 | | 4.768e-07 | | |100.00
Other | | 3.93e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0

46
examples/voronoi/log.27Nov18.voronoi.2d.g++.4 → examples/voronoi/log.6Dec23.voronoi.2d.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (27 Nov 2018)
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Test volume definitions for 2d and finite systems
@ -14,23 +15,23 @@ boundary p p p
#lattice sq 1.0 origin 0.5 0.5 0.0
lattice hex 1.0 origin 0.5 0.5 0.0
Lattice spacing in x,y,z = 1 1.73205 1
Lattice spacing in x,y,z = 1 1.7320508 1
atom_style atomic
region box block 0 ${len} 0 ${len} 0.0 ${lenz}
region box block 0 4 0 ${len} 0.0 ${lenz}
region box block 0 4 0 4 0.0 ${lenz}
region box block 0 4 0 4 0.0 10
region box block 0 ${len} 0 ${len} -0.5 0.5
region box block 0 4 0 ${len} -0.5 0.5
region box block 0 4 0 4 -0.5 0.5
region atoms block 0 ${len} 0 ${len} 0.0 0.0
region atoms block 0 4 0 ${len} 0.0 0.0
region atoms block 0 4 0 4 0.0 0.0
create_box 1 box
Created orthogonal box = (0 0 0) to (4 6.9282 10)
Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
2 by 2 by 1 MPI processor grid
create_atoms 1 region atoms
Created 32 atoms
Time spent = 0.000319481 secs
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
create_atoms CPU = 0.000 seconds
mass 1 1.0
@ -57,9 +58,10 @@ thermo 1
#
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 20
@ -69,12 +71,12 @@ Neighbor list info ...
pair build: half/nsq/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.042 | 3.042 | 3.042 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.038 | 3.038 | 3.038 Mbytes
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 5.1159077e-13
Loop time of 2.79546e-05 on 4 procs for 0 steps with 32 atoms
27.712813 27.712813 27.712813 2.1316282e-14
Loop time of 2.18725e-06 on 4 procs for 0 steps with 32 atoms
51.9% CPU use with 4 MPI tasks x 1 OpenMP threads
45.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -84,7 +86,7 @@ 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 | | 2.795e-05 | | |100.00
Other | | 2.187e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -104,14 +106,16 @@ Dangerous builds = 0
#
change_box all boundary f f p
Changing box ...
run 0
WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 7.678 | 7.678 | 7.678 Mbytes
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.671 | 7.671 | 7.671 Mbytes
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 3.4106051e-13
Loop time of 1.88947e-05 on 4 procs for 0 steps with 32 atoms
27.712813 27.712813 27.712813 3.907985e-14
Loop time of 2.22e-06 on 4 procs for 0 steps with 32 atoms
47.6% CPU use with 4 MPI tasks x 1 OpenMP threads
112.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -121,7 +125,7 @@ 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 | | 1.889e-05 | | |100.00
Other | | 2.22e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0

168
examples/voronoi/log.6Dec23.voronoi.data.g++.1 Normal file
View File

@ -0,0 +1,168 @@
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Exercise different output data options
variable len equal 4.0
variable lenz equal 10.0
dimension 2
units metal
boundary f f p
lattice hex 1.0 origin 0.25 0.25 0.0
Lattice spacing in x,y,z = 1 1.7320508 1
atom_style atomic
region box block 0 ${len} 0 ${len} -0.5 0.5
region box block 0 4 0 ${len} -0.5 0.5
region box block 0 4 0 4 -0.5 0.5
region atoms block 0 ${len} 0 ${len} 0.0 0.0
region atoms block 0 4 0 ${len} 0.0 0.0
region atoms block 0 4 0 4 0.0 0.0
create_box 1 box
Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
1 by 1 by 1 MPI processor grid
create_atoms 1 region atoms
Created 32 atoms
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
create_atoms CPU = 0.000 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 0.0 1.0
neighbor 1.0 nsq
#
# TEST 1:
#
# This compute voronoi generates all three
# types of quantity: per-atom, local, and global
compute v1 all voronoi/atom neighbors yes edge_histo 6
# write voronoi per-atom quantities to a file
dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
# writing voronoi local quantities to a file
dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
# sum up a voronoi per-atom quantity
compute volvor all reduce sum c_v1[1]
variable volsys equal lz*lx*ly
variable err equal c_volvor-v_volsys
# output voronoi global quantities
thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.5
ghost atom cutoff = 3.5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/nsq/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
27.712813 27.712813 27.712813 3.1974423e-14 0 186 12 36 0
Loop time of 7.96e-07 on 1 procs for 0 steps with 32 atoms
125.6% CPU use with 1 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 | | 7.96e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 325 ave 325 max 325 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 325
Ave neighs/atom = 10.15625
Neighbor list builds = 0
Dangerous builds = 0
uncompute v1
uncompute volvor
undump dperatom
undump dlocal
#
# TEST 2:
#
# This compute voronoi generates peratom and local and global quantities
compute v2 all voronoi/atom neighbors yes edge_histo 6
# write voronoi local quantities to a file
dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
# sum up a voronoi local quantity
compute sumarea all reduce sum c_v2[3] inputs local
# output voronoi global quantities
thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.03 | 3.03 | 3.03 Mbytes
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
171.39013 0 186 12 36 0
Loop time of 3.74e-07 on 1 procs for 0 steps with 32 atoms
0.0% CPU use with 1 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 | | 3.74e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 325 ave 325 max 325 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 325
Ave neighs/atom = 10.15625
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Exercise different output data options
variable len equal 4.0
variable lenz equal 10.0
dimension 2
units metal
boundary f f p
lattice hex 1.0 origin 0.25 0.25 0.0
Lattice spacing in x,y,z = 1 1.7320508 1
atom_style atomic
region box block 0 ${len} 0 ${len} -0.5 0.5
region box block 0 4 0 ${len} -0.5 0.5
region box block 0 4 0 4 -0.5 0.5
region atoms block 0 ${len} 0 ${len} 0.0 0.0
region atoms block 0 4 0 ${len} 0.0 0.0
region atoms block 0 4 0 4 0.0 0.0
create_box 1 box
Created orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
2 by 2 by 1 MPI processor grid
create_atoms 1 region atoms
Created 32 atoms
using lattice units in orthogonal box = (0 0 -0.5) to (4 6.9282032 0.5)
create_atoms CPU = 0.000 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 0.0 1.0
neighbor 1.0 nsq
#
# TEST 1:
#
# This compute voronoi generates all three
# types of quantity: per-atom, local, and global
compute v1 all voronoi/atom neighbors yes edge_histo 6
# write voronoi per-atom quantities to a file
dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2]
# writing voronoi local quantities to a file
dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3]
# sum up a voronoi per-atom quantity
compute volvor all reduce sum c_v1[1]
variable volsys equal lz*lx*ly
variable err equal c_volvor-v_volsys
# output voronoi global quantities
thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.5
ghost atom cutoff = 3.5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/nsq/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes
c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
27.712813 27.712813 27.712813 3.907985e-14 0 186 12 36 0
Loop time of 2.21425e-06 on 4 procs for 0 steps with 32 atoms
45.2% 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 | | 2.214e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 24 ave 24 max 24 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 81.25 ave 84 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 325
Ave neighs/atom = 10.15625
Neighbor list builds = 0
Dangerous builds = 0
uncompute v1
uncompute volvor
undump dperatom
undump dlocal
#
# TEST 2:
#
# This compute voronoi generates peratom and local and global quantities
compute v2 all voronoi/atom neighbors yes edge_histo 6
# write voronoi local quantities to a file
dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
# sum up a voronoi local quantity
compute sumarea all reduce sum c_v2[3] inputs local
# output voronoi global quantities
thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 2.921 | 2.921 | 2.921 Mbytes
c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
171.39013 0 186 12 36 0
Loop time of 1.82375e-06 on 4 procs for 0 steps with 32 atoms
82.2% 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 | | 1.824e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 24 ave 24 max 24 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 81.25 ave 84 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 325
Ave neighs/atom = 10.15625
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00