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clean up doc src

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This commit is contained in:
Steve Plimpton
2016-10-06 13:00:46 -06:00
parent 02bfa898ee
commit 493873fb93
458 changed files with 16897 additions and 11014 deletions
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14
examples/voronoi/log.15Feb16.voronoi.2d.g++.1 → examples/voronoi/log.5Oct16.voronoi.2d.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Test volume definitions for 2d and finite systems
variable rcut equal 10.0
@ -63,9 +63,9 @@ Neighbor list info ...
master list distance cutoff = 12
ghost atom cutoff = 20
Memory usage per processor = 2.37519 Mbytes
volvor volsys Volume err
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 5.6843419e-14
Loop time of 3.09944e-06 on 1 procs for 0 steps with 32 atoms
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -77,7 +77,7 @@ 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 | | 3.099e-06 | | |100.00
Other | | 9.537e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -100,9 +100,9 @@ change_box all boundary f f p
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 7.05652 Mbytes
volvor volsys Volume err
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 3.4106051e-13
Loop time of 0 on 1 procs for 0 steps with 32 atoms
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -114,7 +114,7 @@ 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 | | 0 | | | 0.00
Other | | 9.537e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0

14
examples/voronoi/log.15Feb16.voronoi.2d.g++.4 → examples/voronoi/log.5Oct16.voronoi.2d.g++.4
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Test volume definitions for 2d and finite systems
variable rcut equal 10.0
@ -63,9 +63,9 @@ Neighbor list info ...
master list distance cutoff = 12
ghost atom cutoff = 20
Memory usage per processor = 2.41069 Mbytes
volvor volsys Volume err
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 5.1159077e-13
Loop time of 6.19888e-06 on 4 procs for 0 steps with 32 atoms
Loop time of 4.05312e-06 on 4 procs for 0 steps with 32 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -77,7 +77,7 @@ 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 | | 6.199e-06 | | |100.00
Other | | 4.053e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -100,9 +100,9 @@ change_box all boundary f f p
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 7.04625 Mbytes
volvor volsys Volume err
c_volvor v_volsys Volume v_err
277.12813 277.12813 27.712813 3.4106051e-13
Loop time of 2.86102e-06 on 4 procs for 0 steps with 32 atoms
Loop time of 1.90735e-06 on 4 procs for 0 steps with 32 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -114,7 +114,7 @@ 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 | | 2.861e-06 | | |100.00
Other | | 1.907e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0

14
examples/voronoi/log.15Feb16.voronoi.data.g++.1 → examples/voronoi/log.5Oct16.voronoi.data.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Exercise different output data options
variable len equal 4.0
@ -71,9 +71,9 @@ Neighbor list info ...
master list distance cutoff = 3.5
ghost atom cutoff = 3.5
Memory usage per processor = 9.40674 Mbytes
volvor volsys Volume err v1[3] v1[4] v1[5] v1[6] v1[7]
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 1.19209e-06 on 1 procs for 0 steps with 32 atoms
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -85,7 +85,7 @@ 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 | | 1.192e-06 | | |100.00
Other | | 9.537e-07 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -130,9 +130,9 @@ thermo 1
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 8.15503 Mbytes
sumarea v2[3] v2[4] v2[5] v2[6] v2[7]
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 0 on 1 procs for 0 steps with 32 atoms
Loop time of 1.19209e-06 on 1 procs for 0 steps with 32 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -144,7 +144,7 @@ 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 | | 0 | | | 0.00
Other | | 1.192e-06 | | |100.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0

14
examples/voronoi/log.15Feb16.voronoi.data.g++.4 → examples/voronoi/log.5Oct16.voronoi.data.g++.4
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Exercise different output data options
variable len equal 4.0
@ -71,9 +71,9 @@ Neighbor list info ...
master list distance cutoff = 3.5
ghost atom cutoff = 3.5
Memory usage per processor = 9.29039 Mbytes
volvor volsys Volume err v1[3] v1[4] v1[5] v1[6] v1[7]
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 3.99351e-06 on 4 procs for 0 steps with 32 atoms
Loop time of 5.00679e-06 on 4 procs for 0 steps with 32 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -85,7 +85,7 @@ 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 | | 3.994e-06 | | |100.00
Other | | 5.007e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -130,9 +130,9 @@ thermo 1
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 8.03996 Mbytes
sumarea v2[3] v2[4] v2[5] v2[6] v2[7]
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 2.86102e-06 on 4 procs for 0 steps with 32 atoms
Loop time of 1.90735e-06 on 4 procs for 0 steps with 32 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -144,7 +144,7 @@ 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 | | 2.861e-06 | | |100.00
Other | | 1.907e-06 | | |100.00
Nlocal: 8 ave 8 max 8 min
Histogram: 4 0 0 0 0 0 0 0 0 0

134
examples/voronoi/log.15Feb16.voronoi.g++.1 → examples/voronoi/log.5Oct16.voronoi.g++.1
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@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Test of Kawasaki Dynamics on LJ test system
units metal
@ -68,10 +68,10 @@ Neighbor list info ...
master list distance cutoff = 2.3
ghost atom cutoff = 5
binsize = 1.15 -> bins = 9 9 9
Memory usage per processor = 8.24398 Mbytes
r0
Memory usage per processor = 8.74398 Mbytes
c_r0
1000
Loop time of 1.90735e-06 on 1 procs for 0 steps with 4000 atoms
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -83,7 +83,7 @@ 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 | | 1.907e-06 | | |100.00
Other | | 9.537e-07 | | |100.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -115,10 +115,10 @@ variable t2a equal c_r0
variable t2b equal c_r1
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 8.24398 Mbytes
r0 r1
Memory usage per processor = 8.74398 Mbytes
c_r0 c_r1
1000 0
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
Loop time of 0 on 1 procs for 0 steps with 4000 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -130,7 +130,7 @@ 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 | | 0 | | | 0.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -163,10 +163,10 @@ thermo_style custom c_r0
variable t3 equal c_r0
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 8.24398 Mbytes
r0
Memory usage per processor = 8.74398 Mbytes
c_r0
1000
Loop time of 1.90735e-06 on 1 procs for 0 steps with 4000 atoms
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -178,7 +178,7 @@ 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 | | 1.907e-06 | | |100.00
Other | | 9.537e-07 | | |100.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -205,24 +205,24 @@ 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:55)
Memory usage per processor = 6.03036 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.53036 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 12000 0 0 0
0 0 0 12000 0 0 0
Loop time of 0.454023 on 1 procs for 1 steps with 4000 atoms
Loop time of 0.454686 on 1 procs for 1 steps with 4000 atoms
Performance: 0.190 ns/day, 126.118 hours/ns, 2.203 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.190 ns/day, 126.302 hours/ns, 2.199 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0059121 | 0.0059121 | 0.0059121 | 0.0 | 1.30
Pair | 0.0058758 | 0.0058758 | 0.0058758 | 0.0 | 1.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00020099 | 0.00020099 | 0.00020099 | 0.0 | 0.04
Output | 0.44782 | 0.44782 | 0.44782 | 0.0 | 98.63
Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
Other | | 8.702e-05 | | | 0.02
Comm | 0.0001812 | 0.0001812 | 0.0001812 | 0.0 | 0.04
Output | 0.44856 | 0.44856 | 0.44856 | 0.0 | 98.65
Modify | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 0.00
Other | | 6.723e-05 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -243,24 +243,24 @@ 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:55)
Memory usage per processor = 6.03036 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.53036 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 48000 0 0 0
0 0 0 48000 0 0 0
Loop time of 0.473173 on 1 procs for 1 steps with 4000 atoms
Loop time of 0.474271 on 1 procs for 1 steps with 4000 atoms
Performance: 0.183 ns/day, 131.437 hours/ns, 2.113 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.182 ns/day, 131.742 hours/ns, 2.108 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.005954 | 0.005954 | 0.005954 | 0.0 | 1.26
Pair | 0.005832 | 0.005832 | 0.005832 | 0.0 | 1.23
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0002439 | 0.0002439 | 0.0002439 | 0.0 | 0.05
Output | 0.46687 | 0.46687 | 0.46687 | 0.0 | 98.67
Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
Other | | 0.0001042 | | | 0.02
Comm | 0.00016904 | 0.00016904 | 0.00016904 | 0.0 | 0.04
Output | 0.46822 | 0.46822 | 0.46822 | 0.0 | 98.72
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 5.007e-05 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -284,24 +284,24 @@ 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:55)
Memory usage per processor = 6.03036 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.53036 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 48000 0 0 0
0 0 0 48000 0 0 0
Loop time of 0.471937 on 1 procs for 1 steps with 4000 atoms
Loop time of 0.465207 on 1 procs for 1 steps with 4000 atoms
Performance: 0.183 ns/day, 131.094 hours/ns, 2.119 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.186 ns/day, 129.224 hours/ns, 2.150 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0062199 | 0.0062199 | 0.0062199 | 0.0 | 1.32
Pair | 0.006129 | 0.006129 | 0.006129 | 0.0 | 1.32
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00022388 | 0.00022388 | 0.00022388 | 0.0 | 0.05
Output | 0.46539 | 0.46539 | 0.46539 | 0.0 | 98.61
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.823e-05 | | | 0.02
Comm | 0.00016928 | 0.00016928 | 0.00016928 | 0.0 | 0.04
Output | 0.45886 | 0.45886 | 0.45886 | 0.0 | 98.64
Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
Other | | 4.482e-05 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -330,24 +330,24 @@ 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:55)
Memory usage per processor = 6.03036 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.53036 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 12000 0 16000 0
0 0 0 12000 0 16000 0
Loop time of 0.211795 on 1 procs for 1 steps with 2000 atoms
Loop time of 0.196673 on 1 procs for 1 steps with 2000 atoms
Performance: 0.408 ns/day, 58.832 hours/ns, 4.722 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.439 ns/day, 54.631 hours/ns, 5.085 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014911 | 0.0014911 | 0.0014911 | 0.0 | 0.70
Pair | 0.0014789 | 0.0014789 | 0.0014789 | 0.0 | 0.75
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.9884e-05 | 8.9884e-05 | 8.9884e-05 | 0.0 | 0.04
Output | 0.21018 | 0.21018 | 0.21018 | 0.0 | 99.24
Comm | 8.1062e-05 | 8.1062e-05 | 8.1062e-05 | 0.0 | 0.04
Output | 0.19509 | 0.19509 | 0.19509 | 0.0 | 99.20
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.695e-05 | | | 0.02
Other | | 1.907e-05 | | | 0.01
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -398,10 +398,10 @@ thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 6.03036 Mbytes
r0 r1 d5a d5b d5c d5d
Memory usage per processor = 6.53036 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
4000 4000 1 1 1 1
Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
Loop time of 0 on 1 procs for 0 steps with 4000 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -413,7 +413,7 @@ 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 | | 1.192e-06 | | |100.00
Other | | 0 | | | 0.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -465,10 +465,10 @@ set atom 13 x 4.4500000000000001776 y 6.4500000000000001776 z 0.4500000000000000
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 6.53036 Mbytes
r0 r1 d5a d5b d5c d5d
Memory usage per processor = 7.03036 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
4000 4002 0 2 2 2
Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -480,7 +480,7 @@ 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 | | 1.192e-06 | | |100.00
Other | | 9.537e-07 | | |100.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -512,8 +512,8 @@ set atom 13 x 3.25 y 0.25 z 0.25
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 6.53036 Mbytes
r0 r1 d5a d5b d5c d5d
Memory usage per processor = 7.03036 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
4000 4000 1 1 1 1
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
@ -578,10 +578,10 @@ Neighbor list info ...
master list distance cutoff = 2.3
ghost atom cutoff = 5
binsize = 1.15 -> bins = 14 9 9
Memory usage per processor = 11.5794 Mbytes
r0
Memory usage per processor = 12.5794 Mbytes
c_r0
1000
Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms
Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
@ -593,7 +593,7 @@ 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 | | 1.192e-06 | | |100.00
Other | | 9.537e-07 | | |100.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -616,4 +616,4 @@ undump d1
print TEST_DONE
TEST_DONE
Total wall time: 0:00:30
Total wall time: 0:00:06

142
examples/voronoi/log.15Feb16.voronoi.g++.4 → examples/voronoi/log.5Oct16.voronoi.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (15 Feb 2016)
LAMMPS (5 Oct 2016)
# Test of Kawasaki Dynamics on LJ test system
units metal
@ -68,10 +68,10 @@ Neighbor list info ...
master list distance cutoff = 2.3
ghost atom cutoff = 5
binsize = 1.15 -> bins = 9 9 9
Memory usage per processor = 7.70003 Mbytes
r0
Memory usage per processor = 8.20003 Mbytes
c_r0
1000
Loop time of 5.96046e-06 on 4 procs for 0 steps with 4000 atoms
Loop time of 1.29938e-05 on 4 procs for 0 steps with 4000 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -83,7 +83,7 @@ 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 | | 5.96e-06 | | |100.00
Other | | 1.299e-05 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -115,10 +115,10 @@ variable t2a equal c_r0
variable t2b equal c_r1
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 7.70003 Mbytes
r0 r1
Memory usage per processor = 8.20003 Mbytes
c_r0 c_r1
1000 0
Loop time of 3.09944e-06 on 4 procs for 0 steps with 4000 atoms
Loop time of 1.66893e-06 on 4 procs for 0 steps with 4000 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -130,7 +130,7 @@ 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 | | 3.099e-06 | | |100.00
Other | | 1.669e-06 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -163,8 +163,8 @@ thermo_style custom c_r0
variable t3 equal c_r0
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 7.70003 Mbytes
r0
Memory usage per processor = 8.20003 Mbytes
c_r0
1000
Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms
@ -205,24 +205,24 @@ 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:55)
Memory usage per processor = 5.64663 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.14663 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 12000 0 0 0
0 0 0 12000 0 0 0
Loop time of 0.262419 on 4 procs for 1 steps with 4000 atoms
Loop time of 0.277843 on 4 procs for 1 steps with 4000 atoms
Performance: 0.329 ns/day, 72.894 hours/ns, 3.811 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.311 ns/day, 77.179 hours/ns, 3.599 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015318 | 0.0015455 | 0.0015759 | 0.0 | 0.59
Pair | 0.0014799 | 0.0015165 | 0.001543 | 0.1 | 0.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00056005 | 0.00060356 | 0.00064278 | 0.2 | 0.23
Output | 0.26013 | 0.26017 | 0.2602 | 0.0 | 99.14
Modify | 0 | 1.2517e-06 | 2.1458e-06 | 0.1 | 0.00
Other | | 9.871e-05 | | | 0.04
Comm | 0.00051594 | 0.00054592 | 0.00059509 | 0.1 | 0.20
Output | 0.27569 | 0.27571 | 0.27571 | 0.0 | 99.23
Modify | 0 | 4.7684e-07 | 9.5367e-07 | 0.1 | 0.00
Other | | 7.474e-05 | | | 0.03
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -243,24 +243,24 @@ 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:55)
Memory usage per processor = 5.64663 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.14663 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 48000 0 0 0
0 0 0 48000 0 0 0
Loop time of 0.27636 on 4 procs for 1 steps with 4000 atoms
Loop time of 0.275933 on 4 procs for 1 steps with 4000 atoms
Performance: 0.313 ns/day, 76.767 hours/ns, 3.618 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.313 ns/day, 76.648 hours/ns, 3.624 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015159 | 0.001533 | 0.001559 | 0.0 | 0.55
Pair | 0.001452 | 0.0014912 | 0.0015581 | 0.1 | 0.54
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00051785 | 0.00055867 | 0.00060701 | 0.1 | 0.20
Output | 0.27416 | 0.2742 | 0.27422 | 0.0 | 99.22
Modify | 0 | 1.0729e-06 | 1.9073e-06 | 0.1 | 0.00
Other | | 6.926e-05 | | | 0.03
Comm | 0.00044107 | 0.00050235 | 0.00053501 | 0.2 | 0.18
Output | 0.27389 | 0.2739 | 0.27391 | 0.0 | 99.26
Modify | 0 | 4.7684e-07 | 9.5367e-07 | 0.1 | 0.00
Other | | 3.755e-05 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -284,24 +284,24 @@ 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:55)
Memory usage per processor = 5.64663 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.14663 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 48000 0 0 0
0 0 0 48000 0 0 0
Loop time of 0.272119 on 4 procs for 1 steps with 4000 atoms
Loop time of 0.274319 on 4 procs for 1 steps with 4000 atoms
Performance: 0.318 ns/day, 75.589 hours/ns, 3.675 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.315 ns/day, 76.200 hours/ns, 3.645 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015891 | 0.0015998 | 0.0016181 | 0.0 | 0.59
Pair | 0.001529 | 0.0015675 | 0.0016341 | 0.1 | 0.57
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00053191 | 0.00055522 | 0.00059175 | 0.1 | 0.20
Output | 0.26986 | 0.2699 | 0.26992 | 0.0 | 99.18
Modify | 0 | 2.3842e-07 | 9.5367e-07 | 0.1 | 0.00
Other | | 6.658e-05 | | | 0.02
Comm | 0.00042391 | 0.00048423 | 0.00051594 | 0.2 | 0.18
Output | 0.27222 | 0.27223 | 0.27224 | 0.0 | 99.24
Modify | 0 | 4.7684e-07 | 9.5367e-07 | 0.1 | 0.00
Other | | 3.517e-05 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -330,24 +330,24 @@ 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:55)
Memory usage per processor = 5.64663 Mbytes
v1[1] v1[2] v1[3] v1[4] v1[5] v1[6] v1[7]
Memory usage per processor = 6.14663 Mbytes
c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7]
0 0 0 12000 0 16000 0
0 0 0 12000 0 16000 0
Loop time of 0.120695 on 4 procs for 1 steps with 2000 atoms
Loop time of 0.119681 on 4 procs for 1 steps with 2000 atoms
Performance: 0.716 ns/day, 33.526 hours/ns, 8.285 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.722 ns/day, 33.245 hours/ns, 8.356 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00037694 | 0.00038201 | 0.00039315 | 0.0 | 0.32
Pair | 0.00036597 | 0.00036877 | 0.00037217 | 0.0 | 0.31
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00030208 | 0.00031257 | 0.00033903 | 0.1 | 0.26
Output | 0.11993 | 0.11996 | 0.11997 | 0.0 | 99.39
Modify | 0 | 7.1526e-07 | 1.9073e-06 | 0.1 | 0.00
Other | | 4.16e-05 | | | 0.03
Comm | 0.0002737 | 0.00027668 | 0.00027895 | 0.0 | 0.23
Output | 0.11901 | 0.11902 | 0.11902 | 0.0 | 99.45
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.681e-05 | | | 0.01
Nlocal: 500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -398,10 +398,10 @@ thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 5.64663 Mbytes
r0 r1 d5a d5b d5c d5d
Memory usage per processor = 6.14663 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
4000 4000 1 1 1 1
Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms
Loop time of 2.14577e-06 on 4 procs for 0 steps with 4000 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -413,7 +413,7 @@ 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 | | 2.861e-06 | | |100.00
Other | | 2.146e-06 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -465,12 +465,12 @@ set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z 1.4499999999999999
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 6.14663 Mbytes
r0 r1 d5a d5b d5c d5d
Memory usage per processor = 6.64663 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
4000 4002 0 2 2 2
Loop time of 2.74181e-06 on 4 procs for 0 steps with 4000 atoms
Loop time of 4.41074e-06 on 4 procs for 0 steps with 4000 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
5662.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -480,7 +480,7 @@ 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 | | 2.742e-06 | | |100.00
Other | | 4.411e-06 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -512,10 +512,10 @@ set atom 13 x 3.25 y 0.25 z 0.25
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Memory usage per processor = 6.14663 Mbytes
r0 r1 d5a d5b d5c d5d
Memory usage per processor = 6.64663 Mbytes
c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
4000 4000 1 1 1 1
Loop time of 2.6226e-06 on 4 procs for 0 steps with 4000 atoms
Loop time of 2.38419e-06 on 4 procs for 0 steps with 4000 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -527,7 +527,7 @@ 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 | | 2.623e-06 | | |100.00
Other | | 2.384e-06 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -578,10 +578,10 @@ Neighbor list info ...
master list distance cutoff = 2.3
ghost atom cutoff = 5
binsize = 1.15 -> bins = 14 9 9
Memory usage per processor = 7.70784 Mbytes
r0
250
Loop time of 4.29153e-06 on 4 procs for 0 steps with 4000 atoms
Memory usage per processor = 8.20784 Mbytes
c_r0
1000
Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -593,7 +593,7 @@ 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 | | 4.292e-06 | | |100.00
Other | | 2.861e-06 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -607,7 +607,7 @@ 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 -75% 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
@ -616,4 +616,4 @@ undump d1
print TEST_DONE
TEST_DONE
Total wall time: 0:00:11
Total wall time: 0:00:03