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lammps/examples/USER/misc/kolmogorov_crespi/log.atom-diffusion
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LAMMPS (17 Nov 2016)
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
1 by 1 by 1 MPI processor grid
reading atoms ...
129 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
128 atoms in group membrane
group adsorbant type 2
1 atoms in group adsorbant
######################## Potential defition ########################
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
fix thermostat adsorbant nve
fix rigid_membrane membrane setforce 0 0 0
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 100
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 3 3 7
Memory usage per processor = 2.48399 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
200 0.02000000 -0.02562011 -0.02650010 0.05318658 0.00000000 3.31198892
300 0.03000000 -0.02562011 -0.02748822 0.11290898 0.00000000 3.32658305
400 0.04000000 -0.02562011 -0.02868854 0.18545625 0.00000000 3.34632324
500 0.05000000 -0.02562011 -0.02996656 0.26269978 0.00000000 3.37059992
600 0.06000000 -0.02562011 -0.03120006 0.33725276 0.00000000 3.39872815
700 0.07000000 -0.02562011 -0.03229421 0.40338328 0.00000000 3.42999603
800 0.08000000 -0.02562011 -0.03318758 0.45737874 0.00000000 3.46370507
900 0.09000000 -0.02562011 -0.03385069 0.49745690 0.00000000 3.49919977
1000 0.10000000 -0.02562011 -0.03428002 0.52340564 0.00000000 3.53588638
1100 0.11000000 -0.02562011 -0.03449041 0.53612164 0.00000000 3.57324216
1200 0.12000000 -0.02562011 -0.03450775 0.53717016 0.00000000 3.61081749
1300 0.13000000 -0.02562011 -0.03436312 0.52842859 0.00000000 3.64823296
1400 0.14000000 -0.02562011 -0.03408851 0.51183115 0.00000000 3.68517357
1500 0.15000000 -0.02562011 -0.03371417 0.48920613 0.00000000 3.72138134
1600 0.16000000 -0.02562011 -0.03326714 0.46218758 0.00000000 3.75664759
1700 0.17000000 -0.02562011 -0.03277063 0.43217815 0.00000000 3.79080541
1800 0.18000000 -0.02562011 -0.03224395 0.40034589 0.00000000 3.82372274
1900 0.19000000 -0.02562011 -0.03170282 0.36763982 0.00000000 3.85529629
2000 0.20000000 -0.02562011 -0.03115972 0.33481494 0.00000000 3.88544626
2100 0.21000000 -0.02562011 -0.03062440 0.30246010 0.00000000 3.91411185
2200 0.22000000 -0.02562011 -0.03010433 0.27102702 0.00000000 3.94124749
2300 0.23000000 -0.02562011 -0.02960514 0.24085558 0.00000000 3.96681976
2400 0.24000000 -0.02562011 -0.02913096 0.21219623 0.00000000 3.99080483
2500 0.25000000 -0.02562011 -0.02868478 0.18522907 0.00000000 4.01318637
2600 0.26000000 -0.02562011 -0.02826867 0.16007955 0.00000000 4.03395384
2700 0.27000000 -0.02562011 -0.02788403 0.13683143 0.00000000 4.05310113
2800 0.28000000 -0.02562011 -0.02753171 0.11553708 0.00000000 4.07062542
2900 0.29000000 -0.02562011 -0.02721220 0.09622581 0.00000000 4.08652629
3000 0.30000000 -0.02562011 -0.02692571 0.07891041 0.00000000 4.10080498
3100 0.31000000 -0.02562011 -0.02667226 0.06359229 0.00000000 4.11346382
3200 0.32000000 -0.02562011 -0.02645177 0.05026555 0.00000000 4.12450573
3300 0.33000000 -0.02562011 -0.02626406 0.03892009 0.00000000 4.13393390
3400 0.34000000 -0.02562011 -0.02610893 0.02954399 0.00000000 4.14175142
3500 0.35000000 -0.02562011 -0.02598618 0.02212545 0.00000000 4.14796110
3600 0.36000000 -0.02562011 -0.02589566 0.01665409 0.00000000 4.15256529
3700 0.37000000 -0.02562011 -0.02583722 0.01312208 0.00000000 4.15556569
3800 0.38000000 -0.02562011 -0.02581079 0.01152492 0.00000000 4.15696329
3900 0.39000000 -0.02562011 -0.02581636 0.01186148 0.00000000 4.15675830
4000 0.40000000 -0.02562011 -0.02585398 0.01413478 0.00000000 4.15495012
4100 0.41000000 -0.02562011 -0.02592375 0.01835185 0.00000000 4.15153731
4200 0.42000000 -0.02562011 -0.02602587 0.02452390 0.00000000 4.14651764
4300 0.43000000 -0.02562011 -0.02616057 0.03266513 0.00000000 4.13988811
4400 0.44000000 -0.02562011 -0.02632813 0.04279292 0.00000000 4.13164506
4500 0.45000000 -0.02562011 -0.02652889 0.05492664 0.00000000 4.12178432
4600 0.46000000 -0.02562011 -0.02676317 0.06908643 0.00000000 4.11030130
4700 0.47000000 -0.02562011 -0.02703129 0.08529164 0.00000000 4.09719124
4800 0.48000000 -0.02562011 -0.02733352 0.10355859 0.00000000 4.08244950
4900 0.49000000 -0.02562011 -0.02767004 0.12389788 0.00000000 4.06607186
5000 0.50000000 -0.02562011 -0.02804086 0.14631034 0.00000000 4.04805502
5100 0.51000000 -0.02562011 -0.02844575 0.17078211 0.00000000 4.02839708
5200 0.52000000 -0.02562011 -0.02888415 0.19727899 0.00000000 4.00709829
5300 0.53000000 -0.02562011 -0.02935502 0.22573844 0.00000000 3.98416189
5400 0.54000000 -0.02562011 -0.02985670 0.25605986 0.00000000 3.95959511
5500 0.55000000 -0.02562011 -0.03038669 0.28809268 0.00000000 3.93341053
5600 0.56000000 -0.02562011 -0.03094143 0.32162137 0.00000000 3.90562766
5700 0.57000000 -0.02562011 -0.03151597 0.35634628 0.00000000 3.87627492
5800 0.58000000 -0.02562011 -0.03210361 0.39186361 0.00000000 3.84539210
5900 0.59000000 -0.02562011 -0.03269556 0.42764084 0.00000000 3.81303330
6000 0.60000000 -0.02562011 -0.03328042 0.46299030 0.00000000 3.77927044
6100 0.61000000 -0.02562011 -0.03384380 0.49704060 0.00000000 3.74419758
6200 0.62000000 -0.02562011 -0.03436783 0.52871353 0.00000000 3.70793588
6300 0.63000000 -0.02562011 -0.03483104 0.55670974 0.00000000 3.67063945
6400 0.64000000 -0.02562011 -0.03520832 0.57951248 0.00000000 3.63250187
6500 0.65000000 -0.02562011 -0.03547159 0.59542438 0.00000000 3.59376331
6600 0.66000000 -0.02562011 -0.03559125 0.60265655 0.00000000 3.55471782
6700 0.67000000 -0.02562011 -0.03553879 0.59948637 0.00000000 3.51572023
6800 0.68000000 -0.02562011 -0.03529110 0.58451568 0.00000000 3.47719153
6900 0.69000000 -0.02562011 -0.03483635 0.55703035 0.00000000 3.43962129
7000 0.70000000 -0.02562011 -0.03418150 0.51745146 0.00000000 3.40356509
7100 0.71000000 -0.02562011 -0.03336032 0.46781889 0.00000000 3.36963482
7200 0.72000000 -0.02562011 -0.03243997 0.41219328 0.00000000 3.33847933
7300 0.73000000 -0.02562011 -0.03152342 0.35679665 0.00000000 3.31075400
7400 0.74000000 -0.02562011 -0.03074422 0.30970201 0.00000000 3.28707906
7500 0.75000000 -0.02562011 -0.03025182 0.27994115 0.00000000 3.26798907
7600 0.76000000 -0.02562011 -0.03018799 0.27608346 0.00000000 3.25387900
7700 0.77000000 -0.02562011 -0.03065928 0.30456818 0.00000000 3.24495492
7800 0.78000000 -0.02562011 -0.03171321 0.36826788 0.00000000 3.24119821
7900 0.79000000 -0.02562011 -0.03332635 0.46576624 0.00000000 3.24235091
8000 0.80000000 -0.02562011 -0.03540847 0.59160963 0.00000000 3.24792582
8100 0.81000000 -0.02562011 -0.03782107 0.73742737 0.00000000 3.25723999
8200 0.82000000 -0.02562011 -0.04040358 0.89351498 0.00000000 3.26946524
8300 0.83000000 -0.02562011 -0.04299943 1.05040805 0.00000000 3.28368734
8400 0.84000000 -0.02562011 -0.04547588 1.20008497 0.00000000 3.29896495
8500 0.85000000 -0.02562011 -0.04773539 1.33664998 0.00000000 3.31438148
8600 0.86000000 -0.02562011 -0.04971913 1.45654768 0.00000000 3.32908572
8700 0.87000000 -0.02562011 -0.05140498 1.55844058 0.00000000 3.34231951
8800 0.88000000 -0.02562011 -0.05280154 1.64284923 0.00000000 3.35343297
8900 0.89000000 -0.02562011 -0.05394019 1.71166905 0.00000000 3.36188901
9000 0.90000000 -0.02562011 -0.05486563 1.76760281 0.00000000 3.36725955
9100 0.91000000 -0.02562011 -0.05562624 1.81357448 0.00000000 3.36921674
9200 0.92000000 -0.02562011 -0.05626439 1.85214388 0.00000000 3.36752214
9300 0.93000000 -0.02562011 -0.05680723 1.88495335 0.00000000 3.36201704
9400 0.94000000 -0.02562011 -0.05725852 1.91222952 0.00000000 3.35261669
9500 0.95000000 -0.02562011 -0.05759110 1.93233038 0.00000000 3.33931122
9600 0.96000000 -0.02562011 -0.05774152 1.94142215 0.00000000 3.32217490
9700 0.97000000 -0.02562011 -0.05760814 1.93336063 0.00000000 3.30138553
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
131.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
Other | | 0.01361 | | | 3.56
Nlocal: 129 ave 129 max 129 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1867 ave 1867 max 1867 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 290 ave 290 max 290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 290
Ave neighs/atom = 2.24806
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00
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