173 lines
6.8 KiB
Groff
173 lines
6.8 KiB
Groff
LAMMPS (21 Nov 2023)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# REAX potential for Nitroamines system
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# .....
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dimension 3
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boundary p p p
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units real
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atom_style charge
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read_data data.FC
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Reading data file ...
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orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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17280 atoms
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read_data CPU = 0.025 seconds
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pair_style reaxff NULL
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pair_coeff * * ffield.reax.FC C F
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Reading potential file ffield.reax.FC with DATE: 2013-06-28
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WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
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neighbor 2. bin
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neigh_modify every 10 delay 0 check no
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fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
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# should equilibrate much longer in practice
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fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
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timestep 0.2
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thermo_style custom step temp epair etotal press
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thermo 1
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dump 4 all xyz 5000 dumpnpt.xyz
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run 10
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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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- pair reaxff command: doi:10.1016/j.parco.2011.08.005
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@Article{Aktulga12,
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author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
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title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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number = {4--5},
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pages = {245--259}
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}
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- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
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@Article{Aktulga12,
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author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
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title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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pages = {245--259}
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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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Neighbor list info ...
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update: every = 10 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 28 27 17
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair reaxff, perpetual
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attributes: half, newton off, ghost
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pair build: half/bin/newtoff/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(2) fix qeq/reax, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 384.3 | 384.3 | 384.3 Mbytes
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Step Temp E_pair TotEng Press
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0 0 -808525.04 -808525.04 58194.694
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1 4.9935726 -808803.88 -808546.69 58205.825
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2 19.98696 -809640.53 -808611.1 58239.155
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3 45.012616 -811035.3 -808716.9 58294.499
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4 80.103613 -812988.58 -808862.81 58371.548
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5 125.26228 -815500.68 -809049 58469.872
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6 180.4316 -818571.56 -809278.36 58588.936
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7 245.47913 -822200.73 -809557.22 58728.144
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8 320.17692 -826387.19 -809896.34 58886.879
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9 404.17073 -831129.38 -810312.4 59064.554
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10 497.02486 -836425.06 -810825.59 59260.717
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Loop time of 6.13793 on 1 procs for 10 steps with 17280 atoms
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Performance: 0.028 ns/day, 852.491 hours/ns, 1.629 timesteps/s, 28.153 katom-step/s
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99.8% 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 | 5.1752 | 5.1752 | 5.1752 | 0.0 | 84.31
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Neigh | 0.039453 | 0.039453 | 0.039453 | 0.0 | 0.64
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Comm | 0.00042596 | 0.00042596 | 0.00042596 | 0.0 | 0.01
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Output | 0.00064013 | 0.00064013 | 0.00064013 | 0.0 | 0.01
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Modify | 0.92205 | 0.92205 | 0.92205 | 0.0 | 15.02
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Other | | 0.0002045 | | | 0.00
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Nlocal: 17280 ave 17280 max 17280 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5352 ave 5352 max 5352 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2621360
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Ave neighs/atom = 151.69907
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Neighbor list builds = 1
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Dangerous builds not checked
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unfix 1
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fix 1 all nvt temp 100.0 100.0 100.0
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thermo_style custom step temp epair etotal press
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timestep 0.2
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#dump 5 all xyz 5000 dumpnvt.xyz
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#dump 6 all custom 5000 dumpidtype.dat id type x y z
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run 10
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Per MPI rank memory allocation (min/avg/max) = 386.9 | 386.9 | 386.9 Mbytes
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Step Temp E_pair TotEng Press
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10 497.02486 -836425.06 -810825.59 59260.717
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11 601.6514 -841814.09 -810825.78 59489.425
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12 716.37597 -847724.6 -810827.35 59738.298
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13 841.27959 -854161.62 -810831.16 60008.164
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14 976.4666 -861131.68 -810838.36 60300.364
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15 1122.0668 -868642.96 -810850.45 60616.793
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16 1278.2373 -876705.43 -810869.28 60959.942
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17 1445.1655 -885331.03 -810897.18 61332.932
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18 1623.072 -894533.91 -810936.92 61739.541
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19 1812.1864 -904337.86 -811000.45 62200.561
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20 2011.5898 -915379.05 -811771.28 63361.15
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Loop time of 6.11372 on 1 procs for 10 steps with 17280 atoms
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Performance: 0.028 ns/day, 849.127 hours/ns, 1.636 timesteps/s, 28.264 katom-step/s
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99.8% 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 | 5.0783 | 5.0783 | 5.0783 | 0.0 | 83.06
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Neigh | 0.03596 | 0.03596 | 0.03596 | 0.0 | 0.59
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Comm | 0.00041578 | 0.00041578 | 0.00041578 | 0.0 | 0.01
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Output | 0.00062133 | 0.00062133 | 0.00062133 | 0.0 | 0.01
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Modify | 0.99825 | 0.99825 | 0.99825 | 0.0 | 16.33
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Other | | 0.0002171 | | | 0.00
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Nlocal: 17280 ave 17280 max 17280 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5352 ave 5352 max 5352 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2621360
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Ave neighs/atom = 151.69907
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Neighbor list builds = 1
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Dangerous builds not checked
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Total wall time: 0:00:13
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