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log.python.17Mar15.linux.4
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Wed, Jul 31, 02:46
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text/x-python
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Fri, Aug 2, 02:46 (1 d, 23 h)
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rLAMMPS lammps
log.python.17Mar15.linux.4
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LAMMPS (12 Mar 2015)
# 3d Lennard-Jones melt
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
master list distance cutoff = 2.8
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 0.00962114 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00643039 (66.836)
Neigh time (%) = 0.00174427 (18.1296)
Comm time (%) = 0.00106865 (11.1073)
Outpt time (%) = 3.48091e-05 (0.361798)
Other time (%) = 0.000343025 (3.56532)
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
master list distance cutoff = 1.3
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 0.00155491 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.000403821 (25.9708)
Neigh time (%) = 0.00049901 (32.0926)
Comm time (%) = 0.000386357 (24.8476)
Outpt time (%) = 2.87294e-05 (1.84766)
Other time (%) = 0.000236988 (15.2413)
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
master list distance cutoff = 1.4
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 0.00199097 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.000789523 (39.6551)
Neigh time (%) = 0.000541985 (27.2221)
Comm time (%) = 0.000392973 (19.7377)
Outpt time (%) = 2.49147e-05 (1.25138)
Other time (%) = 0.000241578 (12.1336)
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
master list distance cutoff = 1.5
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 0.00233454 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00106812 (45.7528)
Neigh time (%) = 0.000583589 (24.9981)
Comm time (%) = 0.000406563 (17.4152)
Outpt time (%) = 2.41399e-05 (1.03403)
Other time (%) = 0.000252128 (10.7999)
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
master list distance cutoff = 1.6
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 0.00265193 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00123417 (46.5387)
Neigh time (%) = 0.000687182 (25.9125)
Comm time (%) = 0.000449538 (16.9514)
Outpt time (%) = 2.40803e-05 (0.908028)
Other time (%) = 0.000256956 (9.68938)
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
master list distance cutoff = 1.7
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 0.00285125 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00141847 (49.7491)
Neigh time (%) = 0.000675321 (23.6851)
Comm time (%) = 0.000490129 (17.19)
Outpt time (%) = 2.77162e-05 (0.972071)
Other time (%) = 0.000239611 (8.40371)
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
master list distance cutoff = 1.8
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 0.00325108 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00161421 (49.6517)
Neigh time (%) = 0.000730813 (22.4791)
Comm time (%) = 0.000600517 (18.4713)
Outpt time (%) = 2.87294e-05 (0.88369)
Other time (%) = 0.000276804 (8.51423)
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
master list distance cutoff = 1.9
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 0.00360203 on 4 procs for 10 steps with 4000 atoms
Pair time (%) = 0.00191045 (53.0381)
Neigh time (%) = 0.000787675 (21.8676)
Comm time (%) = 0.000629485 (17.4758)
Outpt time (%) = 2.46167e-05 (0.683413)
Other time (%) = 0.000249803 (6.93507)
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
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