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 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 = 0.010 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) = 6.481 | 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 9.7731898 -55.150518 0 -54.060304 322.94195
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Loop time of 2.28421 on 1 procs for 5000 steps with 864 atoms
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Performance: 18912.438 ns/day, 0.001 hours/ns, 2188.940 timesteps/s, 1.891 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 | 1.2715 | 1.2715 | 1.2715 | 0.0 | 55.66
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Bond | 0.00057126 | 0.00057126 | 0.00057126 | 0.0 | 0.03
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Neigh | 0.27008 | 0.27008 | 0.27008 | 0.0 | 11.82
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Comm | 0.057938 | 0.057938 | 0.057938 | 0.0 | 2.54
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Output | 6.1954e-05 | 6.1954e-05 | 6.1954e-05 | 0.0 | 0.00
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Modify | 0.658 | 0.658 | 0.658 | 0.0 | 28.81
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Other | | 0.0261 | | | 1.14
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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 9.7731898 -55.150518 0 -54.060304 322.94195
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6000 10.024842 -55.108242 0 -53.989956 336.6125
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8000 10.118994 -55.092171 0 -53.963382 340.42078
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10000 10.541359 -55.100316 0 -53.924412 340.09986
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12000 10.023234 -55.07343 0 -53.955323 345.70551
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14000 9.5912018 -55.115121 0 -54.045208 333.43739
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16000 9.9450498 -55.077813 0 -53.968428 343.49906
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18000 10.113744 -55.12201 0 -53.993806 332.32214
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20000 9.9345204 -55.176339 0 -54.068128 316.83219
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22000 10.585719 -55.110505 0 -53.929652 336.86599
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24000 10.024757 -55.120592 0 -54.002315 333.13056
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26000 9.7787474 -55.116664 0 -54.02583 332.51437
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28000 9.6092087 -55.130413 0 -54.058491 328.69165
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30000 9.8245787 -55.057678 0 -53.961731 350.86255
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32000 10.066994 -55.08989 0 -53.966902 341.49724
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34000 9.5677059 -55.17222 0 -54.104928 316.06902
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36000 9.7252627 -55.079475 0 -53.994608 343.13769
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38000 10.438984 -55.108991 0 -53.944506 336.32562
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40000 10.238268 -55.080817 0 -53.938723 345.13228
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Loop time of 19.138 on 1 procs for 35000 steps with 864 atoms
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Performance: 15801.041 ns/day, 0.002 hours/ns, 1828.824 timesteps/s, 1.580 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 | 11.568 | 11.568 | 11.568 | 0.0 | 60.44
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Bond | 0.0042372 | 0.0042372 | 0.0042372 | 0.0 | 0.02
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Neigh | 2.2577 | 2.2577 | 2.2577 | 0.0 | 11.80
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Comm | 0.42841 | 0.42841 | 0.42841 | 0.0 | 2.24
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Output | 0.00060128 | 0.00060128 | 0.00060128 | 0.0 | 0.00
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Modify | 4.694 | 4.694 | 4.694 | 0.0 | 24.53
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Other | | 0.1852 | | | 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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