194 lines
7.5 KiB
Groff
194 lines
7.5 KiB
Groff
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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# GJ thermostat
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units metal
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atom_style full
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boundary p p p
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read_data argon.lmp
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Reading data file ...
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orthogonal box = (0 0 0) to (32.146 32.146 32.146)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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864 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.007 seconds
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include ff-argon.lmp
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#############################
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#Atoms types - mass - charge#
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#############################
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#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
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variable Ar equal 1
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#############
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#Atom Masses#
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#############
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mass ${Ar} 39.903
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mass 1 39.903
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###########################
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#Pair Potentials - Tersoff#
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###########################
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pair_style lj/cubic
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pair_coeff * * 0.0102701 3.42
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velocity all create 10 2357 mom yes dist gaussian
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neighbor 1 bin
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timestep 0.1
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compute myKE all ke
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compute myPE all pe
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fix lang all gjf 10 10 1 26488 vel vfull method 1
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run 5000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- GJ methods: doi:10.1080/00268976.2019.1662506
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@Article{gronbech-jensen_complete_2020,
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title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
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volume = {118},
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number = {8},
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url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
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doi = {10.1080/00268976.2019.1662506},
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journal = {Molecular Physics},
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author = {Grønbech-Jensen, Niels},
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year = {2020}
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}
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- GJ-I vfull method: doi:10.1080/00268976.2012.760055
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@Article{gronbech-jensen_simple_2013,
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title = {A simple and effective Verlet-type algorithm for simulating Langevin dynamics},
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volume = {111},
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url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2012.760055},
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doi = {10.1080/00268976.2012.760055},
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pages = {983-991},
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number = {8},
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journal = {Molecular Physics},
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author = {Grønbech-Jensen, Niels and Farago, Oded},
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year = {2013}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.9407173
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ghost atom cutoff = 6.9407173
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binsize = 3.4703587, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 10 -56.207652 0 -55.092137 33.341103
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5000 8.4535562 -55.150518 0 -54.207511 318.20862
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Loop time of 2.26831 on 1 procs for 5000 steps with 864 atoms
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Performance: 19044.977 ns/day, 0.001 hours/ns, 2204.280 timesteps/s, 1.904 Matom-step/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.2802 | 1.2802 | 1.2802 | 0.0 | 56.44
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Bond | 0.00051213 | 0.00051213 | 0.00051213 | 0.0 | 0.02
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Neigh | 0.27007 | 0.27007 | 0.27007 | 0.0 | 11.91
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Comm | 0.057527 | 0.057527 | 0.057527 | 0.0 | 2.54
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Output | 6.3876e-05 | 6.3876e-05 | 6.3876e-05 | 0.0 | 0.00
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Modify | 0.63364 | 0.63364 | 0.63364 | 0.0 | 27.93
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Other | | 0.02635 | | | 1.16
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Nlocal: 864 ave 864 max 864 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1593 ave 1593 max 1593 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 18143 ave 18143 max 18143 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 18143
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Ave neighs/atom = 20.998843
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Ave special neighs/atom = 0
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Neighbor list builds = 258
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Dangerous builds = 0
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fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
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thermo 2000
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run 35000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
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Step Temp E_pair E_mol TotEng Press
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5000 8.4535562 -55.150518 0 -54.207511 318.20862
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6000 8.4899401 -55.108242 0 -54.161176 331.10703
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8000 8.3618893 -55.092171 0 -54.15939 334.11831
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10000 8.8684311 -55.100316 0 -54.111029 334.09931
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12000 8.4339192 -55.07343 0 -54.132614 340.00487
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14000 8.072393 -55.115121 0 -54.214633 327.98965
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16000 8.3420289 -55.077813 0 -54.147247 337.74926
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18000 8.3803911 -55.12201 0 -54.187164 326.10485
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20000 8.4676985 -55.176339 0 -54.231754 311.57092
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22000 8.8560138 -55.110505 0 -54.122603 330.66179
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24000 8.3187826 -55.120592 0 -54.192619 327.01148
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26000 8.0327666 -55.116664 0 -54.220596 326.25179
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28000 8.3672169 -55.130413 0 -54.197037 324.2368
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30000 8.1669275 -55.057678 0 -54.146645 344.9168
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32000 8.3819314 -55.08989 0 -54.154873 335.45317
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34000 8.109088 -55.17222 0 -54.267639 310.83717
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36000 8.3048574 -55.079475 0 -54.153056 338.04291
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38000 8.8708544 -55.108991 0 -54.119434 330.70097
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40000 8.4012779 -55.080817 0 -54.143642 338.54326
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Loop time of 18.9699 on 1 procs for 35000 steps with 864 atoms
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Performance: 15941.040 ns/day, 0.002 hours/ns, 1845.028 timesteps/s, 1.594 Matom-step/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 11.593 | 11.593 | 11.593 | 0.0 | 61.11
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Bond | 0.0041801 | 0.0041801 | 0.0041801 | 0.0 | 0.02
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Neigh | 2.2671 | 2.2671 | 2.2671 | 0.0 | 11.95
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Comm | 0.42339 | 0.42339 | 0.42339 | 0.0 | 2.23
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Output | 0.00062204 | 0.00062204 | 0.00062204 | 0.0 | 0.00
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Modify | 4.4976 | 4.4976 | 4.4976 | 0.0 | 23.71
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Other | | 0.1839 | | | 0.97
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Nlocal: 864 ave 864 max 864 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1592 ave 1592 max 1592 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 18144 ave 18144 max 18144 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 18144
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Ave neighs/atom = 21
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Ave special neighs/atom = 0
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Neighbor list builds = 2122
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Dangerous builds = 0
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Total wall time: 0:00:21
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