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lammps/examples/python/log.5Oct16.python.g++.4
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LAMMPS (5 Oct 2016)
# 3d Lennard-Jones melt with Python functions added
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12
Memory usage per processor = 2.60344 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
Loop time of 0.00930309 on 4 procs for 10 steps with 4000 atoms
Performance: 464361.693 tau/day, 1074.911 timesteps/s
96.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0064399 | 0.0064787 | 0.0065157 | 0.0 | 69.64
Neigh | 0.0017071 | 0.0017205 | 0.0017281 | 0.0 | 18.49
Comm | 0.00073171 | 0.00077122 | 0.00081086 | 0.1 | 8.29
Output | 1.9789e-05 | 2.3663e-05 | 2.9087e-05 | 0.1 | 0.25
Modify | 0.00012827 | 0.00012904 | 0.00013018 | 0.0 | 1.39
Other | | 0.0001799 | | | 1.93
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 2901 ave 2912 max 2888 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 38996 ave 39269 max 38365 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 155984
Ave neighs/atom = 38.996
Neighbor list builds = 1
Dangerous builds = 0
# 1st Python function
# example of catching a syntax error
python simple here """
def simple():
import exceptions
print "Inside simple function"
try:
foo += 1
except Exception, e:
print "FOO error:",e
"""
python simple invoke
# 2nd Python function
# example of returning the function value to a python-style variable
# invoke it twice
variable fact python factorial
python factorial input 1 v_n return v_fact format ii here """
def factorial(n):
if n == 1: return 1
return n*factorial(n-1)
"""
variable n string 10
python factorial invoke
print "Factorial of $n = ${fact}"
Factorial of 10 = 3628800
variable n string 20
python factorial invoke
print "Factorial of $n = ${fact}"
Factorial of 20 = 2432902008176640000
# 3rd Python function
# example of calling back to LAMMPS and writing a run loop in Python
variable cut string 0.0
python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
python loop invoke
pair_style lj/cut ${cut}
pair_style lj/cut 1.0
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 26 26 26
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1259767 0.016557378 0 1.7051002 1.2784679
20 0.87608998 0.39300382 0 1.7068103 6.0488236
Loop time of 0.00152922 on 4 procs for 10 steps with 4000 atoms
Performance: 2824975.566 tau/day, 6539.295 timesteps/s
130.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00040293 | 0.0004105 | 0.00041485 | 0.0 | 26.84
Neigh | 0.00057507 | 0.00060332 | 0.00062108 | 0.1 | 39.45
Comm | 0.0002377 | 0.00025356 | 0.00026774 | 0.1 | 16.58
Output | 1.9073e-05 | 1.9789e-05 | 2.1935e-05 | 0.0 | 1.29
Modify | 0.00012994 | 0.00013161 | 0.00013328 | 0.0 | 8.61
Other | | 0.0001104 | | | 7.22
Nlocal: 1000 ave 1015 max 987 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 943 ave 956 max 928 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 4431.75 ave 4498 max 4325 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 17727
Ave neighs/atom = 4.43175
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.1
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.4
ghost atom cutoff = 1.4
binsize = 0.7 -> bins = 24 24 24
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.87608998 -0.33042884 0 0.9833776 8.5817494
30 1.0155079 -0.83166219 0 0.69121891 7.9905553
Loop time of 0.00186676 on 4 procs for 10 steps with 4000 atoms
Performance: 2314172.647 tau/day, 5356.881 timesteps/s
107.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00075388 | 0.00077951 | 0.00079727 | 0.1 | 41.76
Neigh | 0.00057292 | 0.00058091 | 0.00058484 | 0.0 | 31.12
Comm | 0.00022578 | 0.00024849 | 0.00028563 | 0.1 | 13.31
Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 1.00
Modify | 0.00012493 | 0.00012845 | 0.00013137 | 0.0 | 6.88
Other | | 0.0001107 | | | 5.93
Nlocal: 1000 ave 1019 max 983 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 945.25 ave 962 max 925 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 5259 ave 5343 max 5125 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 21036
Ave neighs/atom = 5.259
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.2
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75 -> bins = 23 23 23
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press
30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
Loop time of 0.00224304 on 4 procs for 10 steps with 4000 atoms
Performance: 1925955.918 tau/day, 4458.231 timesteps/s
89.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010781 | 0.0011036 | 0.0011303 | 0.1 | 49.20
Neigh | 0.00060606 | 0.00060952 | 0.00061703 | 0.0 | 27.17
Comm | 0.00023556 | 0.0002715 | 0.00029659 | 0.1 | 12.10
Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.83
Modify | 0.00012541 | 0.00012833 | 0.00013351 | 0.0 | 5.72
Other | | 0.0001114 | | | 4.97
Nlocal: 1000 ave 1013 max 984 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 1023 ave 1035 max 1005 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 6023.75 ave 6093 max 5953 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 24095
Ave neighs/atom = 6.02375
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.3
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.6
ghost atom cutoff = 1.6
binsize = 0.8 -> bins = 21 21 21
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press
40 1.0490928 -3.0667608 0 -1.493515 6.2796311
50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
Loop time of 0.00257862 on 4 procs for 10 steps with 4000 atoms
Performance: 1675317.210 tau/day, 3878.049 timesteps/s
77.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0012422 | 0.0012776 | 0.0013103 | 0.1 | 49.55
Neigh | 0.0007019 | 0.00072145 | 0.00073099 | 0.0 | 27.98
Comm | 0.00027132 | 0.00031221 | 0.00036168 | 0.2 | 12.11
Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.74
Modify | 0.00012279 | 0.00012654 | 0.00012875 | 0.0 | 4.91
Other | | 0.0001217 | | | 4.72
Nlocal: 1000 ave 1013 max 974 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 1184.75 ave 1200 max 1165 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 6784.25 ave 6922 max 6577 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 27137
Ave neighs/atom = 6.78425
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.4
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7
ghost atom cutoff = 1.7
binsize = 0.85 -> bins = 20 20 20
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press
50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
Loop time of 0.00283062 on 4 procs for 10 steps with 4000 atoms
Performance: 1526164.943 tau/day, 3532.789 timesteps/s
97.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014381 | 0.0014688 | 0.0015128 | 0.1 | 51.89
Neigh | 0.00070405 | 0.000714 | 0.00071907 | 0.0 | 25.22
Comm | 0.00032473 | 0.00037426 | 0.0004046 | 0.2 | 13.22
Output | 1.8835e-05 | 1.961e-05 | 2.1935e-05 | 0.0 | 0.69
Modify | 0.00012612 | 0.00012892 | 0.00013089 | 0.0 | 4.55
Other | | 0.000125 | | | 4.42
Nlocal: 1000 ave 1016 max 981 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 1402.25 ave 1408 max 1390 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 7721.75 ave 7798 max 7615 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 30887
Ave neighs/atom = 7.72175
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.5
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9 -> bins = 19 19 19
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press
60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
70 1.1122144 -3.9657095 0 -2.297805 4.8014106
Loop time of 0.00313491 on 4 procs for 10 steps with 4000 atoms
Performance: 1378031.621 tau/day, 3189.888 timesteps/s
87.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016167 | 0.001663 | 0.0016985 | 0.1 | 53.05
Neigh | 0.00075388 | 0.00076818 | 0.00078201 | 0.0 | 24.50
Comm | 0.00037456 | 0.00042272 | 0.00048018 | 0.2 | 13.48
Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.61
Modify | 0.00012636 | 0.00012881 | 0.00013304 | 0.0 | 4.11
Other | | 0.0001331 | | | 4.25
Nlocal: 1000 ave 1022 max 982 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 1595.75 ave 1604 max 1588 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 8989.75 ave 9204 max 8776 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 35959
Ave neighs/atom = 8.98975
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.6
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.9
ghost atom cutoff = 1.9
binsize = 0.95 -> bins = 18 18 18
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press
70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
80 1.117224 -4.1831357 0 -2.5077187 4.446079
Loop time of 0.00345927 on 4 procs for 10 steps with 4000 atoms
Performance: 1248816.671 tau/day, 2890.779 timesteps/s
79.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0019331 | 0.0019561 | 0.0019834 | 0.0 | 56.55
Neigh | 0.00081587 | 0.00081897 | 0.00082588 | 0.0 | 23.67
Comm | 0.00037837 | 0.00040215 | 0.00041842 | 0.1 | 11.63
Output | 1.812e-05 | 1.9312e-05 | 2.1935e-05 | 0.0 | 0.56
Modify | 0.00012708 | 0.00013059 | 0.00013423 | 0.0 | 3.78
Other | | 0.0001321 | | | 3.82
Nlocal: 1000 ave 1013 max 987 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1706 ave 1720 max 1693 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 10809.8 ave 10831 max 10761 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 43239
Ave neighs/atom = 10.8097
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00
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