193 lines
7.5 KiB
Groff
193 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 2 by 2 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 = 0.002 seconds
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read_data CPU = 0.015 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
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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 vhalf method: doi:10.1080/00268976.2019.1570369
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@Article{jensen_accurate_2019,
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title = {Accurate configurational and kinetic statistics in discrete-time Langevin systems},
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volume = {117},
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url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1570369},
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doi = {10.1080/00268976.2019.1570369},
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number = {18},
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journal = {Molecular Physics},
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author = {Jensen, Lucas Frese Grønbech and Grønbech-Jensen, Niels},
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year = {2019}
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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) = 6.427 | 6.427 | 6.427 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 9.3726166 -55.076514 0 -54.030985 342.43571
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Loop time of 2.11818 on 4 procs for 5000 steps with 864 atoms
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Performance: 20394.822 ns/day, 0.001 hours/ns, 2360.512 timesteps/s, 2.039 Matom-step/s
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63.1% CPU use with 4 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 | 0.53987 | 0.54922 | 0.56044 | 1.2 | 25.93
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Bond | 0.00058281 | 0.00063674 | 0.00075153 | 0.0 | 0.03
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Neigh | 0.10821 | 0.10912 | 0.11017 | 0.2 | 5.15
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Comm | 0.96075 | 0.97484 | 0.98645 | 1.1 | 46.02
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Output | 0.00026318 | 0.00026575 | 0.00027192 | 0.0 | 0.01
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Modify | 0.26142 | 0.2634 | 0.26465 | 0.2 | 12.44
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Other | | 0.2207 | | | 10.42
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Nlocal: 216 ave 216 max 216 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 884.75 ave 885 max 884 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 4536 ave 4737 max 4335 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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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 = 273
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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) = 6.428 | 6.428 | 6.428 Mbytes
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Step Temp E_pair E_mol TotEng Press
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5000 9.3726166 -55.076514 0 -54.030985 342.43571
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6000 9.6911866 -55.129244 0 -54.048177 329.72537
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8000 9.7296551 -55.101417 0 -54.016059 337.46595
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10000 10.098808 -55.083292 0 -53.956755 343.4122
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12000 10.114344 -55.090905 0 -53.962635 341.3438
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14000 10.230012 -55.085051 0 -53.943878 342.45237
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16000 9.5989709 -55.090733 0 -54.019954 339.07584
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18000 10.016071 -55.030131 0 -53.912824 358.79514
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20000 9.7197057 -55.104072 0 -54.019824 335.89619
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22000 9.959647 -55.152019 0 -54.041005 323.05805
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24000 10.075138 -55.115242 0 -53.991345 334.76239
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26000 10.227192 -55.125275 0 -53.984416 332.10131
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28000 10.177109 -55.107097 0 -53.971825 337.32979
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30000 9.521036 -55.099011 0 -54.036925 337.10716
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32000 10.265633 -55.077016 0 -53.93187 346.01018
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34000 10.173978 -55.097068 0 -53.962146 339.63562
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36000 9.6032778 -55.152202 0 -54.080942 321.61646
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38000 9.8802995 -55.048407 0 -53.946245 351.82506
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40000 10.372288 -55.087634 0 -53.93059 343.34304
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Loop time of 17.867 on 4 procs for 35000 steps with 864 atoms
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Performance: 16925.013 ns/day, 0.001 hours/ns, 1958.914 timesteps/s, 1.693 Matom-step/s
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65.3% CPU use with 4 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 | 5.0932 | 5.1683 | 5.2256 | 2.5 | 28.93
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Bond | 0.0044473 | 0.0048347 | 0.0058137 | 0.8 | 0.03
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Neigh | 0.85262 | 0.8601 | 0.87438 | 0.9 | 4.81
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Comm | 6.8164 | 6.8981 | 6.9859 | 2.6 | 38.61
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Output | 0.0046884 | 0.0047093 | 0.0047322 | 0.0 | 0.03
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Modify | 3.4107 | 3.4186 | 3.4248 | 0.3 | 19.13
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Other | | 1.512 | | | 8.47
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Nlocal: 216 ave 222 max 210 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 905.5 ave 911 max 899 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Neighs: 4535.75 ave 4837 max 4218 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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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 = 2140
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Dangerous builds = 0
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Total wall time: 0:00:21
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