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 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 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) = 6.427 | 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 7.946377 -55.076514 0 -54.190084 337.31999
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Loop time of 2.0998 on 4 procs for 5000 steps with 864 atoms
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Performance: 20573.405 ns/day, 0.001 hours/ns, 2381.181 timesteps/s, 2.057 Matom-step/s
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65.2% 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 | 0.53641 | 0.54389 | 0.54721 | 0.6 | 25.90
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Bond | 0.00056487 | 0.0006195 | 0.00068462 | 0.0 | 0.03
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Neigh | 0.10567 | 0.1086 | 0.11128 | 0.7 | 5.17
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Comm | 0.96913 | 0.97758 | 0.98191 | 0.5 | 46.56
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Output | 0.00025213 | 0.00025642 | 0.00026405 | 0.0 | 0.01
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Modify | 0.25061 | 0.25105 | 0.25172 | 0.1 | 11.96
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Other | | 0.2178 | | | 10.37
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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 7.946377 -55.076514 0 -54.190084 337.31999
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6000 8.2565866 -55.129244 0 -54.208209 324.57967
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8000 7.9942397 -55.101417 0 -54.209648 331.24127
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10000 8.5413968 -55.083292 0 -54.130486 337.82599
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12000 8.3682078 -55.090905 0 -54.157419 335.08066
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14000 8.5082065 -55.085051 0 -54.135948 336.2765
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16000 8.1944037 -55.090733 0 -54.176635 334.03786
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18000 8.2607106 -55.030131 0 -54.108637 352.49892
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20000 8.1154691 -55.104072 0 -54.198779 330.14203
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22000 8.5592601 -55.152019 0 -54.197221 318.03507
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24000 8.3182914 -55.115242 0 -54.187324 328.46084
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26000 8.3691375 -55.125275 0 -54.191685 325.43673
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28000 8.531632 -55.107097 0 -54.155381 331.42771
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30000 8.1102222 -55.099011 0 -54.194304 332.04678
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32000 8.5558571 -55.077016 0 -54.122598 339.87746
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34000 8.4213946 -55.097068 0 -54.157649 333.34935
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36000 8.0936615 -55.152202 0 -54.249342 316.20169
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38000 7.999652 -55.048407 0 -54.156034 345.07945
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40000 8.6699753 -55.087634 0 -54.120485 337.23709
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Loop time of 17.6726 on 4 procs for 35000 steps with 864 atoms
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Performance: 17111.263 ns/day, 0.001 hours/ns, 1980.470 timesteps/s, 1.711 Matom-step/s
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65.4% 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 | 5.0739 | 5.1178 | 5.1689 | 1.5 | 28.96
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Bond | 0.0043764 | 0.004688 | 0.0051706 | 0.4 | 0.03
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Neigh | 0.83797 | 0.85506 | 0.87554 | 1.8 | 4.84
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Comm | 6.816 | 6.8932 | 6.9215 | 1.7 | 39.00
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Output | 0.0043624 | 0.0045336 | 0.004998 | 0.4 | 0.03
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Modify | 3.3008 | 3.3033 | 3.3066 | 0.1 | 18.69
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Other | | 1.494 | | | 8.45
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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: 0:00:19
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