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|
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 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
Time spent = 0.000517368 secs
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 ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 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 0.00902343 on 4 procs for 10 steps with 4000 atoms
Performance: 478753.753 tau/day, 1108.226 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0058084 | 0.0058863 | 0.0059605 | 0.1 | 65.23
Neigh | 0.0019183 | 0.0019591 | 0.0020542 | 0.1 | 21.71
Comm | 0.00081086 | 0.00084025 | 0.00090694 | 0.0 | 9.31
Output | 2.1458e-05 | 2.9743e-05 | 4.53e-05 | 0.0 | 0.33
Modify | 0.00015211 | 0.00015229 | 0.00015259 | 0.0 | 1.69
Other | | 0.0001558 | | | 1.73
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 """
from __future__ import print_function
def simple():
foo = 0
print("Inside simple function")
try:
foo += 1
except Exception as 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
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 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 0.00153601 on 4 procs for 10 steps with 4000 atoms
Performance: 2812478.584 tau/day, 6510.367 timesteps/s
91.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00042677 | 0.00043494 | 0.00044322 | 0.0 | 28.32
Neigh | 0.00051236 | 0.00051689 | 0.00052524 | 0.0 | 33.65
Comm | 0.00025344 | 0.00026941 | 0.00027728 | 0.0 | 17.54
Output | 1.7881e-05 | 2.3544e-05 | 3.9339e-05 | 0.0 | 1.53
Modify | 0.00015187 | 0.00015521 | 0.00016356 | 0.0 | 10.10
Other | | 0.000136 | | | 8.86
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
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 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 0.00198567 on 4 procs for 10 steps with 4000 atoms
Performance: 2175589.035 tau/day, 5036.086 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00076985 | 0.00078291 | 0.00079393 | 0.0 | 39.43
Neigh | 0.0005703 | 0.00057709 | 0.00058103 | 0.0 | 29.06
Comm | 0.00030351 | 0.00031525 | 0.00033665 | 0.0 | 15.88
Output | 1.9073e-05 | 2.4378e-05 | 4.0054e-05 | 0.0 | 1.23
Modify | 0.00014806 | 0.00015008 | 0.00015354 | 0.0 | 7.56
Other | | 0.000136 | | | 6.85
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
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 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 0.00232226 on 4 procs for 10 steps with 4000 atoms
Performance: 1860259.570 tau/day, 4306.156 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010829 | 0.0010984 | 0.0011158 | 0.0 | 47.30
Neigh | 0.00060892 | 0.00061285 | 0.00062037 | 0.0 | 26.39
Comm | 0.00027418 | 0.00030226 | 0.00031734 | 0.0 | 13.02
Output | 1.7881e-05 | 2.3305e-05 | 3.8624e-05 | 0.0 | 1.00
Modify | 0.00014758 | 0.00014979 | 0.0001533 | 0.0 | 6.45
Other | | 0.0001357 | | | 5.84
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
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 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 0.00268328 on 4 procs for 10 steps with 4000 atoms
Performance: 1609968.749 tau/day, 3726.780 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0012326 | 0.0012579 | 0.0012789 | 0.1 | 46.88
Neigh | 0.00073671 | 0.00076056 | 0.00077105 | 0.0 | 28.34
Comm | 0.00031805 | 0.00035089 | 0.0003984 | 0.0 | 13.08
Output | 1.7405e-05 | 2.2769e-05 | 3.8147e-05 | 0.0 | 0.85
Modify | 0.00014949 | 0.00015247 | 0.00015497 | 0.0 | 5.68
Other | | 0.0001387 | | | 5.17
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
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 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 0.00504404 on 4 procs for 10 steps with 4000 atoms
Performance: 856455.812 tau/day, 1982.537 timesteps/s
88.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0013909 | 0.001602 | 0.0021472 | 0.8 | 31.76
Neigh | 0.00074077 | 0.00075352 | 0.00076365 | 0.0 | 14.94
Comm | 0.00083065 | 0.0018672 | 0.0025668 | 1.7 | 37.02
Output | 2.1458e-05 | 2.7359e-05 | 4.4346e-05 | 0.0 | 0.54
Modify | 0.00014758 | 0.0001505 | 0.00015235 | 0.0 | 2.98
Other | | 0.0006434 | | | 12.76
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
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 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 0.003398 on 4 procs for 10 steps with 4000 atoms
Performance: 1271335.633 tau/day, 2942.907 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0015702 | 0.0016137 | 0.001651 | 0.1 | 47.49
Neigh | 0.00080371 | 0.00082165 | 0.00084138 | 0.0 | 24.18
Comm | 0.0005908 | 0.00064844 | 0.00071096 | 0.0 | 19.08
Output | 1.7643e-05 | 2.3365e-05 | 4.0293e-05 | 0.0 | 0.69
Modify | 0.00014853 | 0.00015211 | 0.00015593 | 0.0 | 4.48
Other | | 0.0001387 | | | 4.08
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
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 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 0.00420767 on 4 procs for 10 steps with 4000 atoms
Performance: 1026696.317 tau/day, 2376.612 timesteps/s
95.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0019023 | 0.00194 | 0.0019965 | 0.1 | 46.11
Neigh | 0.00088286 | 0.00088775 | 0.00089431 | 0.0 | 21.10
Comm | 0.0010023 | 0.0010559 | 0.0010967 | 0.1 | 25.09
Output | 2.0027e-05 | 2.6524e-05 | 4.53e-05 | 0.0 | 0.63
Modify | 0.00014782 | 0.00015038 | 0.00015473 | 0.0 | 3.57
Other | | 0.0001471 | | | 3.50
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
|
