I just wanted to show you guys how a log file looks like. As I mentioned earlier, the log file has global values(values which correspond to the entire simulation box), plays a crucial role in post-processing of data. Visit my Input and output files blog page, where I have given a brief explanation of this. Here I am going to show you the log file generated by the previous Nickel simulation. Hope this gives you an idea of how a log file looks like.
Log File
region forbox block 0 35.2 0 35.2 0 35.2 units box
#<Refers to an abstract geometric region of space. units box refers to the fact that the size of the box is specified in the units as given in the units command. The name "forbox" refers to the region ID so that you can refer to it somewhere else in this input script.>
create_box 1 forbox #<Create the box>
Created orthogonal box = (0 0 0) to (35.2 35.2 35.2)
1 by 1 by 1 MPI processor grid
#=======================================================================
#<Creates the lattice> <3.52 is the argument for the scale keyword, while the other a1, a2 a3 are the three lattice vectors: This is follwed by the basis commands giving the location of atoms in one unit cell.>
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
#=======================================================================
create_atoms 1 region forbox basis 1 1 basis 2 1 basis 3 1 basis 4 1 units box
Created 4000 atoms
create_atoms CPU = 0.0155411 secs
mass 1 58.69 #<Mass of atom type 1 is 58.69 [mass units grams/mole]>
pair_style eam
#Provide the name of the potential
pair_coeff 1 1 Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11
#=======================================================================
group Ni type 1 #<Group all the Nickel types (nickel type is of type 1). All atoms of type 1 are in group with the name 'Ni'
4000 atoms in group Ni
minimize 1e-25 1e-19 10000 10000 #<Minimize the energy using a conjugate gradient step.
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam, 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) = 5.474 | 5.474 | 5.474 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -17800 0 -17800 -0.1203861
2 0 -17800 0 -17800 -0.1203861
Loop time of 0.171891 on 1 procs for 2 steps with 4000 atoms
81.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-17800.0000143 -17800.0000143 -17800.0000143
Force two-norm initial, final = 1.89504e-12 1.79872e-12
Force max component initial, final = 4.4225e-14 4.80033e-14
Final line search alpha, max atom move = 1 4.80033e-14
Iterations, force evaluations = 2 4
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14053 | 0.14053 | 0.14053 | 0.0 | 81.75
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 | | 0.03136 | | | 18.25
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5841 ave 5841 max 5841 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 268000 ave 268000 max 268000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 268000
Ave neighs/atom = 67
Neighbor list builds = 0
Dangerous builds = 0
print "Finished Minimizing"
Finished Minimizing
#minimize etol ftol maxiter for minimizer maxiter for force_energy valuation
variable ener equal pe
#=========================================================
timestep 0.001
velocity all create 300 102939 dist gaussian mom yes rot yes
# Set the velocities of all the atoms so that the temperature of the system
# is 300K. Make the distribution Gaussian.
fix 1 all nve
dump dump_1 all custom 100 dump.in id type x y z ix iy iz vx vy vz #<Dump all the atoms to the file dump.in>
variable poten equal pe-${ener}
variable poten equal pe--17800.0000142793
thermo_style custom step time temp pe ke etotal press vol v_poten
#What to print in the logfile.txt?
#=========================================================
thermo 100 #How frequently to print the thermodynamic information#
run 10000 # run with active settings as many runs as required. timestep*No. of. steps =10ps
Per MPI rank memory allocation (min/avg/max) = 4.349 | 4.349 | 4.349 Mbytes
Step Time Temp PotEng KinEng TotEng Press Volume v_poten
2 0 300 -17800 155.0734 -17644.927 3797.6474 43614.208 1.0913936e-11
100 0.098 168.19503 -17731.837 86.941916 -17644.895 10850.608 43614.208 68.163366
200 0.198 138.54564 -17716.503 71.615811 -17644.887 12414.788 43614.208 83.496995
300 0.298 140.52568 -17717.527 72.639313 -17644.888 12287.653 43614.208 82.473101
400 0.398 148.11005 -17721.45 76.55976 -17644.891 11826.777 43614.208 78.549544
500 0.498 150.03551 -17722.447 77.555052 -17644.892 11681.246 43614.208 77.552744
600 0.598 150.68974 -17722.784 77.893231 -17644.891 11727.42 43614.208 77.215554
700 0.698 151.68844 -17723.302 78.409472 -17644.892 11610.958 43614.208 76.698298
800 0.798 142.15664 -17718.373 73.482376 -17644.891 12110.33 43614.208 81.627038
900 0.898 146.90413 -17720.828 75.936408 -17644.892 11859.48 43614.208 79.171983
1000 0.998 152.36031 -17723.649 78.756771 -17644.892 11574.426 43614.208 76.350935
1100 1.098 146.35145 -17720.541 75.650721 -17644.89 11945.1 43614.208 79.459057
1200 1.198 147.24692 -17721.005 76.113601 -17644.891 11875.792 43614.208 78.995387
1300 1.298 150.14759 -17722.505 77.612991 -17644.892 11692.448 43614.208 77.494972
1400 1.398 154.0402 -17724.518 79.625124 -17644.893 11490.129 43614.208 75.482013
1500 1.498 153.95783 -17724.475 79.582544 -17644.892 11529.453 43614.208 75.525281
1600 1.598 146.65629 -17720.698 75.808298 -17644.89 11943.606 43614.208 79.301592
1700 1.698 149.39146 -17722.113 77.222137 -17644.891 11772.292 43614.208 77.886828
1800 1.798 148.43346 -17721.618 76.726934 -17644.891 11819.613 43614.208 78.38204
1900 1.898 150.56442 -17722.721 77.828454 -17644.892 11684.113 43614.208 77.279412
2000 1.998 155.46215 -17725.253 80.360145 -17644.893 11444.123 43614.208 74.747179
2100 2.098 153.32224 -17724.146 79.254003 -17644.892 11583.632 43614.208 75.854259
2200 2.198 148.72913 -17721.771 76.879772 -17644.891 11793.753 43614.208 78.2292
2300 2.298 150.38045 -17722.625 77.733357 -17644.891 11717.641 43614.208 77.375375
2400 2.398 148.94509 -17721.883 76.991405 -17644.892 11772.397 43614.208 78.117041
2500 2.498 148.43275 -17721.618 76.726568 -17644.891 11782.315 43614.208 78.38196
2600 2.598 148.06121 -17721.425 76.534514 -17644.891 11834.677 43614.208 78.574861
2700 2.698 153.42962 -17724.201 79.309506 -17644.892 11532.829 43614.208 75.798526
2800 2.798 148.30956 -17721.554 76.662891 -17644.891 11768.555 43614.208 78.44569
2900 2.898 152.95636 -17723.957 79.064872 -17644.892 11574.512 43614.208 76.043009
3000 2.998 153.90203 -17724.446 79.553701 -17644.892 11533.742 43614.208 75.554119
3100 3.098 147.78494 -17721.283 76.391709 -17644.891 11822.518 43614.208 78.716952
3200 3.198 144.85245 -17719.767 74.875869 -17644.891 11977.807 43614.208 80.233498
3300 3.298 149.44542 -17722.141 77.250028 -17644.891 11773.463 43614.208 77.85912
3400 3.398 151.69406 -17723.304 78.412379 -17644.892 11618.045 43614.208 76.695781
3500 3.498 150.03615 -17722.447 77.555387 -17644.891 11735.022 43614.208 77.553443
3600 3.598 155.4659 -17725.254 80.362082 -17644.892 11451.688 43614.208 74.745743
3700 3.698 153.34045 -17724.155 79.263414 -17644.892 11561.509 43614.208 75.844656
3800 3.798 154.02334 -17724.508 79.616409 -17644.892 11525.887 43614.208 75.491626
3900 3.898 147.89913 -17721.342 76.450736 -17644.891 11848.686 43614.208 78.658455
4000 3.998 148.40334 -17721.602 76.711368 -17644.891 11813.499 43614.208 78.39761
4100 4.098 149.27721 -17722.054 77.16308 -17644.891 11804.118 43614.208 77.945955
4200 4.198 151.69124 -17723.302 78.410918 -17644.892 11645.973 43614.208 76.697521
4300 4.298 151.99693 -17723.461 78.568932 -17644.892 11626.853 43614.208 76.539119
4400 4.398 149.77156 -17722.31 77.418615 -17644.892 11737.948 43614.208 77.689877
4500 4.498 149.83597 -17722.343 77.451908 -17644.891 11742.852 43614.208 77.656847
4600 4.598 147.36143 -17721.064 76.172789 -17644.891 11850.551 43614.208 78.936153
4700 4.698 147.40234 -17721.085 76.193937 -17644.891 11864.003 43614.208 78.915187
4800 4.798 150.19256 -17722.528 77.636234 -17644.892 11719.793 43614.208 77.472207
4900 4.898 150.14524 -17722.503 77.611775 -17644.892 11711.623 43614.208 77.49671
5000 4.998 149.81174 -17722.331 77.439384 -17644.892 11706.428 43614.208 77.668992
5100 5.098 152.03165 -17723.479 78.586879 -17644.892 11615.821 43614.208 76.521047
5200 5.198 150.28025 -17722.573 77.681563 -17644.891 11729.935 43614.208 77.427187
5300 5.298 149.68005 -17722.263 77.37131 -17644.891 11755.013 43614.208 77.737403
5400 5.398 151.89276 -17723.407 78.515087 -17644.892 11617.748 43614.208 76.592725
5500 5.498 149.14684 -17721.987 77.095691 -17644.891 11753.285 43614.208 78.012992
5600 5.598 152.39592 -17723.667 78.775179 -17644.892 11599.311 43614.208 76.33303
5700 5.698 151.75627 -17723.336 78.444536 -17644.891 11642.865 43614.208 76.664193
5800 5.798 148.32024 -17721.559 76.66841 -17644.891 11810.972 43614.208 78.44063
5900 5.898 148.49223 -17721.648 76.757313 -17644.891 11797.788 43614.208 78.352004
6000 5.998 152.50451 -17723.723 78.831309 -17644.892 11594.098 43614.208 76.276959
6100 6.098 154.83539 -17724.929 80.036167 -17644.892 11467.686 43614.208 75.071409
6200 6.198 149.98052 -17722.418 77.526626 -17644.892 11697.118 43614.208 77.581639
6300 6.298 154.82259 -17724.922 80.029547 -17644.893 11471.282 43614.208 75.077945
6400 6.398 152.69414 -17723.821 78.929332 -17644.892 11585.236 43614.208 76.178671
6500 6.498 151.35472 -17723.128 78.23697 -17644.891 11680.425 43614.208 76.871954
6600 6.598 148.10481 -17721.448 76.557052 -17644.891 11820.464 43614.208 78.552187
6700 6.698 148.68612 -17721.749 76.857541 -17644.891 11762.436 43614.208 78.251086
6800 6.798 147.38642 -17721.077 76.185709 -17644.891 11842.966 43614.208 78.9235
6900 6.898 150.11878 -17722.49 77.598098 -17644.891 11690.596 43614.208 77.51044
7000 6.998 152.86574 -17723.91 79.018033 -17644.892 11551.765 43614.208 76.089993
7100 7.098 150.60452 -17722.74 77.849182 -17644.891 11699.497 43614.208 77.259595
7200 7.198 152.11393 -17723.521 78.629411 -17644.892 11609.588 43614.208 76.478823
7300 7.298 146.88095 -17720.815 75.924427 -17644.891 11873.397 43614.208 79.185028
7400 7.398 149.95607 -17722.405 77.513991 -17644.891 11717.235 43614.208 77.594959
7500 7.498 149.57852 -17722.21 77.318829 -17644.891 11744.93 43614.208 77.790177
7600 7.598 151.41517 -17723.16 78.268216 -17644.892 11623.682 43614.208 76.840134
7700 7.698 151.789 -17723.353 78.461455 -17644.892 11626.981 43614.208 76.646816
7800 7.798 150.3752 -17722.622 77.730644 -17644.891 11718.031 43614.208 77.378089
7900 7.898 149.58652 -17722.215 77.322966 -17644.892 11724.279 43614.208 77.785508
8000 7.998 148.44542 -17721.624 76.733121 -17644.891 11808.965 43614.208 78.376125
8100 8.098 153.25861 -17724.113 79.221113 -17644.892 11547.918 43614.208 75.886708
8200 8.198 151.87231 -17723.397 78.504514 -17644.892 11624.927 43614.208 76.603347
8300 8.298 148.60851 -17721.708 76.817419 -17644.891 11816.443 43614.208 78.291905
8400 8.398 150.12818 -17722.494 77.602957 -17644.891 11735.205 43614.208 77.506127
8500 8.498 150.24654 -17722.555 77.664139 -17644.891 11730.75 43614.208 77.444621
8600 8.598 150.17861 -17722.521 77.629026 -17644.892 11704.534 43614.208 77.479304
8700 8.698 154.54424 -17724.778 79.885667 -17644.893 11468.354 43614.208 75.221572
8800 8.798 147.79559 -17721.288 76.397211 -17644.891 11825.798 43614.208 78.711761
8900 8.898 148.45321 -17721.628 76.737147 -17644.891 11794.686 43614.208 78.371814
9000 8.998 152.33373 -17723.634 78.743028 -17644.891 11595.657 43614.208 76.36552
9100 9.098 148.09314 -17721.442 76.551022 -17644.891 11818.511 43614.208 78.558448
9200 9.198 150.03622 -17722.447 77.555418 -17644.892 11707.304 43614.208 77.553065
9300 9.298 148.91434 -17721.867 76.975509 -17644.891 11776.772 43614.208 78.133415
9400 9.398 150.22033 -17722.542 77.650591 -17644.891 11693.821 43614.208 77.457937
9500 9.498 149.71583 -17722.281 77.389807 -17644.892 11709.75 43614.208 77.718623
9600 9.598 149.44104 -17722.139 77.247763 -17644.891 11748.278 43614.208 77.861176
9700 9.698 147.64891 -17721.212 76.321392 -17644.89 11842.637 43614.208 78.788407
9800 9.798 148.47698 -17721.64 76.749434 -17644.89 11818.395 43614.208 78.360224
9900 9.898 152.654 -17723.801 78.908582 -17644.892 11569.271 43614.208 76.1995
10000 9.998 149.74646 -17722.297 77.40564 -17644.891 11714.251 43614.208 77.703031
10002 10 149.91724 -17722.385 77.493919 -17644.891 11706.689 43614.208 77.614661
Loop time of 254.132 on 1 procs for 10000 steps with 4000 atoms
Performance: 3.400 ns/day, 7.059 hours/ns, 39.350 timesteps/s
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 240.43 | 240.43 | 240.43 | 0.0 | 94.61
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.4389 | 1.4389 | 1.4389 | 0.0 | 0.57
Output | 10.306 | 10.306 | 10.306 | 0.0 | 4.06
Modify | 1.2227 | 1.2227 | 1.2227 | 0.0 | 0.48
Other | | 0.7346 | | | 0.29
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5841 ave 5841 max 5841 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 268000 ave 268000 max 268000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 268000
Ave neighs/atom = 67
Neighbor list builds = 0
Dangerous builds = 0
undump dump_1 # Stop dumping information to the dump file.
unfix 1
# Unfix the NVE. Additional lines if any will assume that this
# fix is off.
Total wall time: 0:04:16
Explanation
If you observe log file you can see 2 sets of value.
The first set:
0 0 -17800 0 -17800 -0.1203861
2 0 -17800 0 -17800 -0.1203861
As the first line suggests, these are time step, temperature, energy and pressure value. These values correspond to energy minimisation step which I have initiated (please look at the input script in my previous post). From this, it is clear that the energy minimisation took 2-time steps. Each time step is 0.001 picoseconds or 1 femtosecond. Thus our energy minimisation process took 2 femtoseconds.
The second set:
Step Time Temp PotEng KinEng TotEng Press Volume v_poten
2 0 300 -17800 155.0734 -17644.927 3797.6474 43614.208 1.0913936e-11
100 0.098 168.19503 -17731.837 86.941916 -17644.895 10850.608 43614.208 68.163366
200 0.198 138.54564 -17716.503 71.615811 -17644.887 12414.788 43614.208 83.496995
(I am just showing 3 sets of values for explanation purpose)
As the first line suggests, these are time step, time, temperature, energy, pressure, volume values. If you notice my thermo_style command in my previous blog, I would have mentioned the exact values as command, and thus LAMMPS printed these values in our log file. These values correspond to the NVE equilibration process. The equilibration process runs for 10002 timesteps(effectively 10000 steps since the first 2 steps are of energy minimisation) because I have given 10000 timesteps in my run command. So LAMMPS stops printing values after 10002 steps. Also if you can see the values are printed for every 100 timesteps, because in my thermo_style command I have given printing frequency as 100. I have run the equilibration process for 10000 timesteps ie. 10000 femtoseconds or 10 picoseconds.
Cumulatively the entire simulation studies 10002 femtoseconds or 10.002 picoseconds. As I have mentioned earlier LAMMPS work in small timescales, which are useful in crack propagation, traditional damage studies and many phenomena which happens in a scale of picoseconds in real-time, whose experimental studies are highly expensive and difficult.
You can use this file for your post-processing like you can import your lof file to Matlab or you can copy-paste these values in an excel sheet and you can plot a graph of temperature or pressure or whatever property variation and you can study that variation. In my previous blog on Argon, I have plotted a temperature variation graph. Like this, you can study various properties.
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