147 lines
5.5 KiB
Groff
147 lines
5.5 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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# This example demonstrates the use of various fix qeq variants with pair reaxff
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# You can comment in/out various versions below
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#
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# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
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# used with pair_style reaxff, provided that the QEq parameters are the same.
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#
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# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
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# the QEq parameters are the same. These two styles can also be used with
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# pair_style reaxff.
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units real
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atom_style charge
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read_data data.CHO
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Reading data file ...
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orthogonal box = (0 0 0) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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105 atoms
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read_data CPU = 0.000 seconds
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pair_style reaxff NULL checkqeq no
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pair_coeff * * ffield.reax.cho H C O
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Reading potential file ffield.reax.cho with DATE: 2011-02-18
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neighbor 1 bin
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neigh_modify every 1 delay 0 check yes
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group type1 type 1
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60 atoms in group type1
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compute charge1 type1 property/atom q
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compute q1 type1 reduce ave c_charge1
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group type2 type 2
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25 atoms in group type2
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compute charge2 type2 property/atom q
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compute q2 type2 reduce ave c_charge2
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group type3 type 3
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20 atoms in group type3
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compute charge3 type3 property/atom q
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compute q3 type3 reduce ave c_charge3
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variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
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thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
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thermo 1
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velocity all create 300.0 1281937
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fix 1 all nve
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fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
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#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
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#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
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#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
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timestep 0.25
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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 = 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 = 11
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ghost atom cutoff = 11
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binsize = 5.5, bins = 5 5 5
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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) = 9.845 | 10.57 | 11.28 Mbytes
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Step PotEng c_q1 c_q2 c_q3 v_qtot
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0 -10226.557 0.095633904 -0.15658758 -0.091167237 -8.8817842e-16
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1 -10225.799 0.095650278 -0.1566235 -0.091171458 -1.7763568e-15
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2 -10223.656 0.095669806 -0.15666728 -0.091175321 0
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3 -10220.276 0.095691215 -0.15671588 -0.091178792 1.7763568e-15
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4 -10215.894 0.09571392 -0.15676795 -0.091181826 1.7763568e-15
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5 -10210.804 0.095734058 -0.15681436 -0.091184227 1.3322676e-15
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6 -10205.342 0.095751113 -0.15685409 -0.091185731 -4.4408921e-16
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7 -10199.848 0.095762524 -0.15688062 -0.091186803 -1.3322676e-15
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8 -10194.646 0.095766647 -0.15689045 -0.091186875 2.8865799e-15
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9 -10190.016 0.095760978 -0.15687772 -0.09118579 -4.4408921e-16
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10 -10186.168 0.095747037 -0.15684594 -0.091183687 -1.5543122e-15
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Loop time of 0.00732332 on 4 procs for 10 steps with 105 atoms
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Performance: 29.495 ns/day, 0.814 hours/ns, 1365.500 timesteps/s, 143.378 katom-step/s
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99.2% 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 | 0.0033186 | 0.0038166 | 0.0041063 | 0.5 | 52.12
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0002671 | 0.00057126 | 0.0010608 | 0.0 | 7.80
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Output | 0.00019157 | 0.0002237 | 0.00028058 | 0.0 | 3.05
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Modify | 0.0026446 | 0.0026528 | 0.0026604 | 0.0 | 36.22
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Other | | 5.9e-05 | | | 0.81
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Nlocal: 26.25 ave 35 max 15 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Nghost: 300 ave 357 max 239 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 1025.25 ave 1468 max 405 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 4101
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Ave neighs/atom = 39.057143
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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