update example inputs and logs for change in ReaxFF required name
This commit is contained in:
Axel Kohlmeyer
33
examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
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33
examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
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## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
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#The default system size may take a while to run you can change to a smaller size
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variable x_rep equal 5 #x-direction replication number
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variable y_rep equal 5 #y-direction replication number
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variable z_rep equal 10 #z-direction replication number
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variable temperature equal 110.0 #Target quantum temperature (K in real units)
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variable delta_t equal 0.25 #MD timestep length (fs in real units)
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variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
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variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
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variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
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variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
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variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
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variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
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##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
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include methane_qtb.mod
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##Shock compression with quantum nuclear corrections
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reset_timestep 0
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fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
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fix_modify shock energy yes
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variable dhug equal f_shock[1]
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variable dray equal f_shock[2]
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variable lgr_vel equal f_shock[3]
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variable lgr_pos equal f_shock[4]
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variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
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thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
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thermo 20
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timestep ${delta_t}
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#restart 1000 restart
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run 500
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@ -0,0 +1,280 @@
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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 script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
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#The default system size may take a while to run you can change to a smaller size
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variable x_rep equal 5 #x-direction replication number
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variable y_rep equal 5 #y-direction replication number
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variable z_rep equal 10 #z-direction replication number
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variable temperature equal 110.0 #Target quantum temperature (K in real units)
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variable delta_t equal 0.25 #MD timestep length (fs in real units)
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variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
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variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
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variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
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variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
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variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
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variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
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##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
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include methane_qtb.mod
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## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
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## This part defines units, methane structure, and atomic information
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#General
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units real
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dimension 3
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boundary p p p
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atom_style charge
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#Lattice
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lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
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Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
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#Computational Cell
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region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
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create_box 2 simbox
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Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
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Created 5 atoms
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using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
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create_atoms CPU = 0.000 seconds
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replicate ${x_rep} ${y_rep} ${z_rep}
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replicate 5 ${y_rep} ${z_rep}
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replicate 5 5 ${z_rep}
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replicate 5 5 10
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Replication is creating a 5x5x10 = 250 times larger system...
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orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
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1 by 1 by 1 MPI processor grid
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1250 atoms
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replicate CPU = 0.000 seconds
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#Atomic Information
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mass 1 12.011150
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mass 2 1.007970
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## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
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#Pair Potentials
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pair_style reaxff NULL
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pair_coeff * * ffield.reax C H
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fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
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#Neighbor Style
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neighbor 2.5 bin
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neigh_modify every 10 delay 0 check no
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## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
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#Initialization
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velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
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velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
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#Setup output
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thermo_style custom step temp press etotal vol
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thermo 20
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#Colored thermal bath
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fix scapegoat_qtb all nve #NVE does the time integration
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fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
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fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
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fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
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timestep ${delta_t}
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timestep 0.25
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run 500 #500 fs
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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 = 12.5
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ghost atom cutoff = 12.5
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binsize = 6.25, bins = 4 4 7
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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) = 201.3 | 201.3 | 201.3 Mbytes
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Step Temp Press TotEng Volume
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0 110 -15717.706 -110869.31 15741.751
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20 133.92166 8773.5364 -110569.51 15741.751
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40 184.43244 -12136.835 -110378.92 15741.751
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60 203.58164 6527.2188 -110190.9 15741.751
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80 183.0518 -9667.6163 -110095.24 15741.751
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100 236.07378 4393.5089 -109905.8 15741.751
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120 226.94599 -5612.6845 -109708.46 15741.751
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140 249.34156 988.50573 -109631.88 15741.751
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160 255.08331 -1397.98 -109469.09 15741.751
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180 281.64743 -1682.598 -109285.53 15741.751
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200 303.76929 2594.8345 -109206.84 15741.751
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220 311.6547 -4566.4307 -109053.21 15741.751
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240 350.68316 5132.0272 -108918.26 15741.751
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260 347.11102 -6078.5078 -108828.31 15741.751
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280 366.56298 6373.2426 -108694.64 15741.751
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300 393.62524 -6438.9321 -108521.5 15741.751
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320 403.64821 5946.6873 -108487.83 15741.751
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340 406.12883 -5053.5592 -108331.25 15741.751
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360 450.60139 4323.0942 -108185.06 15741.751
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380 429.46056 -3317.8604 -108146.84 15741.751
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400 448.11876 3264.6165 -108048.01 15741.751
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420 485.98657 -3047.3542 -107882.88 15741.751
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440 463.23761 3088.3325 -107853.09 15741.751
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460 504.27223 -1966.5888 -107689.56 15741.751
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480 515.66783 2915.6322 -107550.83 15741.751
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500 516.26369 -1733.2701 -107498.06 15741.751
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Loop time of 41.4818 on 1 procs for 500 steps with 1250 atoms
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Performance: 0.260 ns/day, 92.182 hours/ns, 12.053 timesteps/s, 15.067 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 | 30.707 | 30.707 | 30.707 | 0.0 | 74.03
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Neigh | 2.2815 | 2.2815 | 2.2815 | 0.0 | 5.50
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Comm | 0.023963 | 0.023963 | 0.023963 | 0.0 | 0.06
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Output | 0.00073327 | 0.00073327 | 0.00073327 | 0.0 | 0.00
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Modify | 8.4653 | 8.4653 | 8.4653 | 0.0 | 20.41
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Other | | 0.00334 | | | 0.01
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Nlocal: 1250 ave 1250 max 1250 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 8444 ave 8444 max 8444 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 601915 ave 601915 max 601915 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 601915
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Ave neighs/atom = 481.532
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Neighbor list builds = 50
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Dangerous builds not checked
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unfix methane_qtb
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unfix scapegoat_qtb
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##Shock compression with quantum nuclear corrections
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reset_timestep 0
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fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
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fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
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fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
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fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
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fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
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fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
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fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
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fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
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QBMSST parameters:
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Shock in z direction
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Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
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Shock velocity = 1.22000e-01
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Artificial viscosity (units of mass/length/time) = 9.00000e-01
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Initial pressure calculated on first step
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Initial volume calculated on first step
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Initial energy calculated on first step
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fix_modify shock energy yes
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variable dhug equal f_shock[1]
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variable dray equal f_shock[2]
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variable lgr_vel equal f_shock[3]
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variable lgr_pos equal f_shock[4]
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variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
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thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
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thermo 20
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timestep ${delta_t}
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timestep 0.25
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#restart 1000 restart
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run 500
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Fix QBMSST v0 = 1.57418e+04
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Fix QBMSST p0 = -3.03801e+03
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Fix QBMSST e0 = to be -1.07498e+05
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Fix QBMSST initial strain rate of -1.02043e-04 established by reducing temperature by factor of 1.00000e-02
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Per MPI rank memory allocation (min/avg/max) = 201.4 | 201.4 | 201.4 Mbytes
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Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
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0 110 -1789.091 -107498.06 15741.751 19.891812 19.891812 39.783624 -3095.1546 1.9543098e-12 -57.148468 0 0
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20 110 313.41128 -107231.57 15733.908 19.891812 19.891812 39.763803 1026.815 -35.805172 3755.1834 6.0783853e-05 -0.60983919
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40 110 1248.5771 -107106.23 15726.494 19.891812 19.891812 39.745066 -277.53233 -52.672766 2158.1479 0.00011824041 -1.219383
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60 110 -944.55947 -107017.75 15719.482 19.891812 19.891812 39.727345 1006.8843 -64.550247 3165.7346 0.00017258388 -1.8286479
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80 110 2164.646 -107053.82 15712.848 19.891812 19.891812 39.710579 686.99949 -59.728513 2583.9345 0.00022399951 -2.4376489
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100 110 -332.40946 -106996.04 15706.579 19.891812 19.891812 39.694734 1555.274 -67.472889 3204.6947 0.00027258815 -3.0464001
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120 110 2556.8172 -106828.33 15700.655 19.891812 19.891812 39.679765 -1406.2492 -90.123866 9.330762 0.00031849257 -3.6549157
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140 110 -649.1633 -106851.95 15695.029 19.891812 19.891812 39.665545 3704.8784 -86.742267 4898.3193 0.00036209988 -4.2632077
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160 110 2301.4774 -106787.04 15689.738 19.891812 19.891812 39.652174 -893.31294 -95.690383 91.247096 0.00040310452 -4.8712886
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180 110 -701.59672 -106639.61 15684.711 19.891812 19.891812 39.63947 3211.2065 -115.27944 3997.3199 0.00044206086 -5.47917
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200 110 3857.6228 -106696.51 15679.975 19.891812 19.891812 39.627501 -1722.9124 -107.93584 -1123.778 0.00047876602 -6.0868625
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220 110 -1057.1346 -106590.95 15675.462 19.891812 19.891812 39.616094 3285.0876 -121.80821 3706.0326 0.00051374575 -6.6943761
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240 110 2748.5299 -106428.9 15671.216 19.891812 19.891812 39.605364 172.15717 -143.78629 425.48974 0.00054664912 -7.3017201
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260 110 64.99143 -106442.23 15667.188 19.891812 19.891812 39.595183 981.21139 -141.94851 1075.4979 0.00057787086 -7.9089043
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280 110 1612.9607 -106412.77 15663.362 19.891812 19.891812 39.585514 662.48897 -145.93658 605.73218 0.00060752164 -8.5159364
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300 110 1435.9566 -106307.06 15659.725 19.891812 19.891812 39.576323 759.46794 -160.13403 559.12791 0.00063570794 -9.1228243
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320 110 -890.72712 -106332.6 15656.258 19.891812 19.891812 39.56756 234.14376 -156.75496 -103.07714 0.00066257852 -9.7295747
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340 110 4270.0983 -106252.72 15652.976 19.891812 19.891812 39.559265 5411.2268 -167.0427 4944.423 0.00068801647 -10.336194
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360 110 -2801.0763 -106105.96 15649.905 19.891812 19.891812 39.551504 -3276.3824 -187.5258 -3864.4213 0.00071181569 -10.942691
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380 110 5566.9116 -106139.88 15646.926 19.891812 19.891812 39.543977 2737.1121 -182.43141 2031.4929 0.00073489745 -11.549071
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400 110 -4432.9416 -106074.79 15644.09 19.891812 19.891812 39.536808 -4946.1908 -191.90759 -5763.8068 0.00075688314 -12.155339
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420 52.599535 5582.8126 -105959.96 15641.311 19.891812 19.891812 39.529786 7869.5301 -206.09135 6942.2136 0.00077841805 -12.761497
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||||
440 52.599535 -2861.6332 -106017.66 15638.758 19.891812 19.891812 39.523335 -1820.4742 -199.30721 -2848.5648 0.00079820063 -13.367553
|
||||
460 52.599535 3942.7505 -105984.45 15636.294 19.891812 19.891812 39.517106 3327.0393 -203.24794 2201.6559 0.00081729985 -13.973511
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||||
480 52.599535 419.18442 -105827.32 15633.955 19.891812 19.891812 39.511194 -1910.6109 -224.9021 -3128.3482 0.00083542949 -14.579377
|
||||
500 52.599535 117.60016 -105904.83 15631.655 19.891812 19.891812 39.505383 -603.40365 -214.36236 -1911.9203 0.00085325005 -15.185153
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Loop time of 41.8312 on 1 procs for 500 steps with 1250 atoms
|
||||
|
||||
Performance: 0.258 ns/day, 92.958 hours/ns, 11.953 timesteps/s, 14.941 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 31.016 | 31.016 | 31.016 | 0.0 | 74.15
|
||||
Neigh | 2.2849 | 2.2849 | 2.2849 | 0.0 | 5.46
|
||||
Comm | 0.020391 | 0.020391 | 0.020391 | 0.0 | 0.05
|
||||
Output | 0.0019403 | 0.0019403 | 0.0019403 | 0.0 | 0.00
|
||||
Modify | 8.505 | 8.505 | 8.505 | 0.0 | 20.33
|
||||
Other | | 0.003238 | | | 0.01
|
||||
|
||||
Nlocal: 1250 ave 1250 max 1250 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8489 ave 8489 max 8489 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 606382 ave 606382 max 606382 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 606382
|
||||
Ave neighs/atom = 485.1056
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:01:23
|
||||
@ -0,0 +1,280 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
|
||||
#The default system size may take a while to run you can change to a smaller size
|
||||
variable x_rep equal 5 #x-direction replication number
|
||||
variable y_rep equal 5 #y-direction replication number
|
||||
variable z_rep equal 10 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
|
||||
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
|
||||
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
|
||||
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
include methane_qtb.mod
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
||||
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
||||
Created 5 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 5 ${y_rep} ${z_rep}
|
||||
replicate 5 5 ${z_rep}
|
||||
replicate 5 5 10
|
||||
Replication is creating a 5x5x10 = 250 times larger system...
|
||||
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
1250 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 20
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
||||
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
run 500 #500 fs
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 4 4 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 125.2 | 125.3 | 125.4 Mbytes
|
||||
Step Temp Press TotEng Volume
|
||||
0 110 -15717.706 -110869.31 15741.751
|
||||
20 133.92621 9503.0083 -110548.47 15741.751
|
||||
40 188.1524 -13687.131 -110344.93 15741.751
|
||||
60 205.85747 8421.3906 -110165.58 15741.751
|
||||
80 185.08989 -11337.006 -110026.24 15741.751
|
||||
100 245.36524 5805.0694 -109841.66 15741.751
|
||||
120 218.83661 -7740.8838 -109674.15 15741.751
|
||||
140 254.6075 3396.3936 -109589.89 15741.751
|
||||
160 262.20963 -3574.2575 -109413.81 15741.751
|
||||
180 297.89271 917.40867 -109204.79 15741.751
|
||||
200 315.54026 -371.17448 -109129.45 15741.751
|
||||
220 323.90745 -2811.4367 -108988.12 15741.751
|
||||
240 358.28478 3972.8358 -108848.95 15741.751
|
||||
260 359.12673 -6289.689 -108788.08 15741.751
|
||||
280 376.47656 6851.3186 -108664.07 15741.751
|
||||
300 404.30975 -7805.7238 -108482.75 15741.751
|
||||
320 410.9097 7696.2518 -108421.87 15741.751
|
||||
340 406.19092 -8175.1703 -108311.84 15741.751
|
||||
360 460.37085 7630.6182 -108139.6 15741.751
|
||||
380 413.96355 -7515.2307 -108150.73 15741.751
|
||||
400 452.17428 7148.0954 -108027.39 15741.751
|
||||
420 467.1725 -6662.4113 -107842.71 15741.751
|
||||
440 481.03775 6117.6862 -107759.03 15741.751
|
||||
460 509.03937 -4095.0215 -107648.46 15741.751
|
||||
480 533.22373 2211.9169 -107481.89 15741.751
|
||||
500 517.71195 -214.23969 -107489.48 15741.751
|
||||
Loop time of 22.2711 on 4 procs for 500 steps with 1250 atoms
|
||||
|
||||
Performance: 0.485 ns/day, 49.491 hours/ns, 22.451 timesteps/s, 28.063 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.689 | 15.195 | 16.732 | 27.7 | 68.23
|
||||
Neigh | 1.5325 | 1.5496 | 1.5658 | 1.0 | 6.96
|
||||
Comm | 0.073366 | 1.6105 | 3.116 | 85.1 | 7.23
|
||||
Output | 0.00052192 | 0.00057642 | 0.00073657 | 0.0 | 0.00
|
||||
Modify | 3.896 | 3.9129 | 3.9306 | 0.6 | 17.57
|
||||
Other | | 0.00241 | | | 0.01
|
||||
|
||||
Nlocal: 312.5 ave 317 max 308 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 4982 ave 4995 max 4967 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 172509 ave 174182 max 170676 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 690037
|
||||
Ave neighs/atom = 552.0296
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
|
||||
##Shock compression with quantum nuclear corrections
|
||||
reset_timestep 0
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
|
||||
Shock velocity = 1.22000e-01
|
||||
Artificial viscosity (units of mass/length/time) = 9.00000e-01
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 20
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
#restart 1000 restart
|
||||
run 500
|
||||
Fix QBMSST v0 = 1.57418e+04
|
||||
Fix QBMSST p0 = -5.88788e+01
|
||||
Fix QBMSST e0 = to be -1.07489e+05
|
||||
Fix QBMSST initial strain rate of -1.02186e-04 established by reducing temperature by factor of 1.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 126.1 | 126.1 | 126.1 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 110 -270.21489 -107489.48 15741.751 19.891812 19.891812 39.783624 -118.93551 0 -60.056661 0 0
|
||||
20 110 -2180.5877 -107208.2 15733.847 19.891812 19.891812 39.763648 223.47326 -37.773571 -29.703539 6.1258507e-05 -0.60983836
|
||||
40 110 5004.864 -107109.95 15726.306 19.891812 19.891812 39.744592 3335.6341 -50.920246 2784.77 0.00011969641 -1.2193771
|
||||
60 110 -4549.1199 -106949.22 15719.136 19.891812 19.891812 39.72647 -4461.4212 -72.656651 -5295.3675 0.00017526726 -1.8286321
|
||||
80 110 6695.6833 -106942.12 15712.214 19.891812 19.891812 39.708976 5333.2741 -73.356417 4226.043 0.00022891479 -2.4376137
|
||||
100 110 -5337.7671 -106930.78 15705.644 19.891812 19.891812 39.692373 -2682.4224 -75.129348 -4049.0157 0.00027982924 -3.0463347
|
||||
120 110 6526.5587 -106736.15 15699.334 19.891812 19.891812 39.676424 7038.2375 -100.8809 5422.5046 0.00032873694 -3.6548061
|
||||
140 110 -3284.0472 -106761.36 15693.36 19.891812 19.891812 39.661329 -3999.8116 -97.977739 -5851.3636 0.00037502973 -4.2630401
|
||||
160 110 4792.0537 -106662.24 15687.56 19.891812 19.891812 39.64667 4484.6905 -110.86184 2404.1579 0.00041998006 -4.8710464
|
||||
180 110 -1253.5849 -106532.38 15682.037 19.891812 19.891812 39.632711 -723.78287 -128.58314 -3022.3825 0.00046278801 -5.4788331
|
||||
200 110 3276.2225 -106488.13 15676.725 19.891812 19.891812 39.619286 5117.4749 -134.15782 2609.1518 0.00050395806 -6.0864105
|
||||
220 110 -553.17982 -106421.17 15671.675 19.891812 19.891812 39.606524 -1360.8796 -143.56979 -4068.5641 0.00054309397 -6.6937871
|
||||
240 110 1329.8793 -106309.56 15666.794 19.891812 19.891812 39.594187 775.35326 -158.40869 -2125.0508 0.00058092605 -7.300972
|
||||
260 110 1809.8974 -106360.42 15662.075 19.891812 19.891812 39.582262 3075.2725 -151.39659 -11.4097 0.00061749364 -7.9079706
|
||||
280 110 24.534819 -106310.46 15657.56 19.891812 19.891812 39.570852 1043.8352 -158.25965 -2221.0935 0.00065248454 -8.5147908
|
||||
300 110 2854.2862 -106150.2 15653.217 19.891812 19.891812 39.559874 3727.6844 -179.54521 291.27132 0.00068614803 -9.1214393
|
||||
320 110 -776.61228 -106199.04 15649.041 19.891812 19.891812 39.549322 -1285.3999 -173.42703 -4886.655 0.00071850756 -9.7279234
|
||||
340 110 3778.2238 -106201.03 15644.958 19.891812 19.891812 39.539001 3694.462 -172.6926 -68.017561 0.00075015694 -10.334247
|
||||
360 110 -1505.9413 -106025.15 15641.031 19.891812 19.891812 39.529078 -1491.3768 -196.81063 -5408.8787 0.00078058882 -10.940416
|
||||
380 110 3414.9599 -106071.49 15637.176 19.891812 19.891812 39.519335 4956.6752 -189.93327 886.98409 0.00081046454 -11.546435
|
||||
400 110 -947.2273 -106003.34 15633.49 19.891812 19.891812 39.510021 726.91825 -199.51619 -3488.2795 0.0008390284 -12.152307
|
||||
420 46.681884 1610.2414 -105884.37 15629.905 19.891812 19.891812 39.500961 -1377.8364 -215.72223 -5734.5653 0.00086681188 -12.758039
|
||||
440 46.681884 2290.4653 -105923.83 15626.371 19.891812 19.891812 39.492029 6296.7177 -209.55961 1800.4591 0.00089420243 -13.363632
|
||||
460 46.681884 -2068.0472 -105879.44 15622.969 19.891812 19.891812 39.483432 -5629.8405 -216.88862 -10260.4 0.00092056659 -13.969092
|
||||
480 46.681884 5011.06 -105748.92 15619.556 19.891812 19.891812 39.474805 8649.5097 -232.72756 3884.1859 0.00094702163 -14.574419
|
||||
500 46.681884 -3314.8335 -105829.23 15616.305 19.891812 19.891812 39.46659 -5120.4784 -223.60669 -10014.132 0.00097221364 -15.179618
|
||||
Loop time of 26.5748 on 4 procs for 500 steps with 1250 atoms
|
||||
|
||||
Performance: 0.406 ns/day, 59.055 hours/ns, 18.815 timesteps/s, 23.519 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.259 | 18.109 | 19.999 | 31.1 | 68.14
|
||||
Neigh | 1.8265 | 1.8477 | 1.8638 | 1.0 | 6.95
|
||||
Comm | 0.045073 | 1.9349 | 3.7845 | 95.1 | 7.28
|
||||
Output | 0.0019058 | 0.0019666 | 0.0021202 | 0.2 | 0.01
|
||||
Modify | 4.6619 | 4.6782 | 4.699 | 0.6 | 17.60
|
||||
Other | | 0.002774 | | | 0.01
|
||||
|
||||
Nlocal: 312.5 ave 318 max 307 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 5059 ave 5080 max 5039 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 173854 ave 176807 max 170839 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 695414
|
||||
Ave neighs/atom = 556.3312
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:49
|
||||
@ -1,33 +0,0 @@
|
||||
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
|
||||
#The default system size may take a while to run you can change to a smaller size
|
||||
variable x_rep equal 5 #x-direction replication number
|
||||
variable y_rep equal 5 #y-direction replication number
|
||||
variable z_rep equal 10 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
|
||||
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
|
||||
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
|
||||
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
include methane_qtb.mod
|
||||
|
||||
|
||||
##Shock compression with quantum nuclear corrections
|
||||
reset_timestep 0
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 100
|
||||
timestep ${delta_t}
|
||||
restart 1000 restart
|
||||
run 5000
|
||||
@ -3,62 +3,62 @@
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 100
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 20
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 2000 #500 fs
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 500 #500 fs
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
Normal file
70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
Normal file
@ -0,0 +1,70 @@
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 50
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 1000
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1
Normal file
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1
Normal file
@ -0,0 +1,174 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
||||
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
||||
Created 5 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 2 ${z_rep}
|
||||
replicate 2 2 2
|
||||
Replication is creating a 2x2x2 = 8 times larger system...
|
||||
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
40 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 50
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
||||
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 2 2 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 82.45 | 82.45 | 82.45 Mbytes
|
||||
Step Temp Press TotEng Volume
|
||||
0 110 -15746.508 -3548.1354 503.73603
|
||||
50 191.27715 -7523.7503 -3530.4179 503.73603
|
||||
100 214.09982 12016.892 -3517.4544 503.73603
|
||||
150 317.38272 3098.2254 -3499.5793 503.73603
|
||||
200 338.76362 -4484.9241 -3490.3649 503.73603
|
||||
250 402.05826 3973.0488 -3474.81 503.73603
|
||||
300 340.80076 11193.4 -3470.8029 503.73603
|
||||
350 556.19747 8086.3266 -3451.5937 503.73603
|
||||
400 566.8737 5499.5505 -3439.2335 503.73603
|
||||
450 643.2883 -8270.5736 -3426.0767 503.73603
|
||||
500 613.09742 -12406.229 -3419.8547 503.73603
|
||||
550 669.28891 -9757.601 -3410.7281 503.73603
|
||||
600 600.66922 10407.403 -3408.3776 503.73603
|
||||
650 573.1485 30971.977 -3405.0744 503.73603
|
||||
700 726.22146 29573.798 -3386.3167 503.73603
|
||||
750 777.22659 13265.88 -3378.8462 503.73603
|
||||
800 652.46476 -9231.9331 -3388.7229 503.73603
|
||||
850 679.18414 -19802.254 -3384.6321 503.73603
|
||||
900 711.60594 -18792.396 -3373.2944 503.73603
|
||||
950 865.79013 -2837.6042 -3363.2971 503.73603
|
||||
1000 884.14995 6160.4875 -3360.6295 503.73603
|
||||
Loop time of 7.87 on 1 procs for 1000 steps with 40 atoms
|
||||
|
||||
Performance: 2.745 ns/day, 8.744 hours/ns, 127.065 timesteps/s, 5.083 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.3662 | 6.3662 | 6.3662 | 0.0 | 80.89
|
||||
Neigh | 0.97757 | 0.97757 | 0.97757 | 0.0 | 12.42
|
||||
Comm | 0.013653 | 0.013653 | 0.013653 | 0.0 | 0.17
|
||||
Output | 0.00042319 | 0.00042319 | 0.00042319 | 0.0 | 0.01
|
||||
Modify | 0.50971 | 0.50971 | 0.50971 | 0.0 | 6.48
|
||||
Other | | 0.00248 | | | 0.03
|
||||
|
||||
Nlocal: 40 ave 40 max 40 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2552 ave 2552 max 2552 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 25110 ave 25110 max 25110 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 25110
|
||||
Ave neighs/atom = 627.75
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:07
|
||||
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
Normal file
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
Normal file
@ -0,0 +1,174 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
||||
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
||||
Created 5 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 2 ${z_rep}
|
||||
replicate 2 2 2
|
||||
Replication is creating a 2x2x2 = 8 times larger system...
|
||||
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
40 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 50
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
||||
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 2 2 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 72.47 | 72.47 | 72.47 Mbytes
|
||||
Step Temp Press TotEng Volume
|
||||
0 110 -15746.508 -3548.1354 503.73603
|
||||
50 183.74482 -917.59204 -3534.8518 503.73603
|
||||
100 200.96363 16464.403 -3517.1456 503.73603
|
||||
150 255.33305 14801.963 -3507.7299 503.73603
|
||||
200 328.11626 5119.3618 -3498.0388 503.73603
|
||||
250 356.88626 -11306.151 -3485.1746 503.73603
|
||||
300 284.7363 -25276.091 -3479.4732 503.73603
|
||||
350 434.79382 -23326.29 -3471.7491 503.73603
|
||||
400 414.69602 2800.9047 -3465.7225 503.73603
|
||||
450 464.61242 20775.398 -3449.1675 503.73603
|
||||
500 671.43369 15272.581 -3433.9453 503.73603
|
||||
550 534.01157 -8545.4173 -3427.6672 503.73603
|
||||
600 512.69648 -15904.052 -3417.8071 503.73603
|
||||
650 604.62051 -1777.9242 -3419.4324 503.73603
|
||||
700 650.2196 20108.199 -3415.8902 503.73603
|
||||
750 677.45644 21721.335 -3409.1253 503.73603
|
||||
800 707.98295 171.53756 -3413.4048 503.73603
|
||||
850 740.68522 -23846.627 -3384.7024 503.73603
|
||||
900 739.55514 -22742.841 -3377.091 503.73603
|
||||
950 769.44821 -7060.9388 -3389.817 503.73603
|
||||
1000 987.6246 -0.47618437 -3373.9263 503.73603
|
||||
Loop time of 6.80367 on 4 procs for 1000 steps with 40 atoms
|
||||
|
||||
Performance: 3.175 ns/day, 7.560 hours/ns, 146.980 timesteps/s, 5.879 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1801 | 5.3491 | 5.5417 | 6.1 | 78.62
|
||||
Neigh | 0.76934 | 0.77281 | 0.77567 | 0.3 | 11.36
|
||||
Comm | 0.072213 | 0.26492 | 0.4339 | 27.2 | 3.89
|
||||
Output | 0.00032365 | 0.00035547 | 0.00044739 | 0.0 | 0.01
|
||||
Modify | 0.41139 | 0.41424 | 0.4179 | 0.4 | 6.09
|
||||
Other | | 0.00226 | | | 0.03
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1950 ave 1950 max 1950 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6434.5 ave 6447 max 6427 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 25738
|
||||
Ave neighs/atom = 643.45
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:06
|
||||
@ -1,70 +0,0 @@
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 100
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 3000 #750 fs
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
@ -1,19 +1,19 @@
|
||||
# This example demonstrates the use of various fix qeq variants with pair reax/c
|
||||
# This example demonstrates the use of various fix qeq variants with pair reaxff
|
||||
# You can comment in/out various versions below
|
||||
#
|
||||
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||
# used with pair_style reax/c, provided that the QEq parameters are the same.
|
||||
# used with pair_style reaxff, provided that the QEq parameters are the same.
|
||||
#
|
||||
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||
# the QEq parameters are the same. These two styles can also be used with
|
||||
# pair_style reax/c.
|
||||
# pair_style reaxff.
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.CHO
|
||||
|
||||
pair_style reax/c NULL checkqeq no
|
||||
pair_style reaxff NULL checkqeq no
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
|
||||
neighbor 1 bin
|
||||
@ -1,116 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# This example demonstrates the use of various fix qeq variants with pair reax/c
|
||||
# You can comment in/out various versions below
|
||||
#
|
||||
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||
# used with pair_style reax/c, provided that the QEq parameters are the same.
|
||||
#
|
||||
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||
# the QEq parameters are the same. These two styles can also be used with
|
||||
# pair_style reax/c.
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.CHO
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c NULL checkqeq no
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
group type1 type 1
|
||||
60 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
group type2 type 2
|
||||
25 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
group type3 type 3
|
||||
20 atoms in group type3
|
||||
compute charge3 type3 property/atom q
|
||||
compute q3 type3 reduce ave c_charge3
|
||||
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
||||
|
||||
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
||||
thermo 1
|
||||
|
||||
velocity all create 300.0 1281937
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
||||
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
||||
|
||||
timestep 0.25
|
||||
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.65 | 16.65 | 16.65 Mbytes
|
||||
Step PotEng c_q1 c_q2 c_q3 v_qtot
|
||||
0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16
|
||||
1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15
|
||||
2 -10223.656 0.095669731 -0.15666714 -0.091175264 -6.4392935e-15
|
||||
3 -10220.276 0.095691257 -0.15671597 -0.091178813 2.6645353e-15
|
||||
4 -10215.894 0.095714363 -0.15676887 -0.091182006 -3.1086245e-15
|
||||
5 -10210.804 0.095733863 -0.15681398 -0.09118412 6.6613381e-16
|
||||
6 -10205.342 0.095751253 -0.15685427 -0.091185918 -1.110223e-15
|
||||
7 -10199.848 0.095762028 -0.1568795 -0.091186707 8.8817842e-15
|
||||
8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15
|
||||
9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16
|
||||
10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15
|
||||
Loop time of 0.0322483 on 1 procs for 10 steps with 105 atoms
|
||||
|
||||
Performance: 6.698 ns/day, 3.583 hours/ns, 310.094 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.026229 | 0.026229 | 0.026229 | 0.0 | 81.34
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 5.2214e-05 | 5.2214e-05 | 5.2214e-05 | 0.0 | 0.16
|
||||
Output | 0.00027299 | 0.00027299 | 0.00027299 | 0.0 | 0.85
|
||||
Modify | 0.0056667 | 0.0056667 | 0.0056667 | 0.0 | 17.57
|
||||
Other | | 2.694e-05 | | | 0.08
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3417 ave 3417 max 3417 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3417
|
||||
Ave neighs/atom = 32.5429
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,116 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# This example demonstrates the use of various fix qeq variants with pair reax/c
|
||||
# You can comment in/out various versions below
|
||||
#
|
||||
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||
# used with pair_style reax/c, provided that the QEq parameters are the same.
|
||||
#
|
||||
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||
# the QEq parameters are the same. These two styles can also be used with
|
||||
# pair_style reax/c.
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.CHO
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c NULL checkqeq no
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
group type1 type 1
|
||||
60 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
group type2 type 2
|
||||
25 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
group type3 type 3
|
||||
20 atoms in group type3
|
||||
compute charge3 type3 property/atom q
|
||||
compute q3 type3 reduce ave c_charge3
|
||||
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
||||
|
||||
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
||||
thermo 1
|
||||
|
||||
velocity all create 300.0 1281937
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
||||
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
||||
|
||||
timestep 0.25
|
||||
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.83 | 11.69 | 12.52 Mbytes
|
||||
Step PotEng c_q1 c_q2 c_q3 v_qtot
|
||||
0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15
|
||||
1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15
|
||||
2 -10223.656 0.095669684 -0.15666698 -0.091175327 1.110223e-15
|
||||
3 -10220.276 0.095691296 -0.15671615 -0.091178696 0
|
||||
4 -10215.894 0.09571384 -0.15676787 -0.091181678 8.8817842e-16
|
||||
5 -10210.804 0.095734178 -0.15681468 -0.09118418 1.3322676e-15
|
||||
6 -10205.342 0.095751126 -0.15685409 -0.091185769 4.4408921e-16
|
||||
7 -10199.848 0.095762403 -0.15688037 -0.091186751 0
|
||||
8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16
|
||||
9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16
|
||||
10 -10186.168 0.095747223 -0.15684634 -0.091183742 0
|
||||
Loop time of 0.0185181 on 4 procs for 10 steps with 105 atoms
|
||||
|
||||
Performance: 11.664 ns/day, 2.058 hours/ns, 540.011 timesteps/s
|
||||
92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0097179 | 0.01078 | 0.012052 | 0.8 | 58.21
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00041604 | 0.0017492 | 0.0028496 | 2.1 | 9.45
|
||||
Output | 0.00041103 | 0.00046283 | 0.00051498 | 0.0 | 2.50
|
||||
Modify | 0.0051849 | 0.0052357 | 0.0052917 | 0.1 | 28.27
|
||||
Other | | 0.0002902 | | | 1.57
|
||||
|
||||
Nlocal: 26.25 ave 35 max 15 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 300 ave 357 max 239 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1025.25 ave 1468 max 405 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 4101
|
||||
Ave neighs/atom = 39.0571
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
146
examples/qeq/log.30Nov23.reaxff.g++.1
Normal file
146
examples/qeq/log.30Nov23.reaxff.g++.1
Normal file
@ -0,0 +1,146 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# This example demonstrates the use of various fix qeq variants with pair reaxff
|
||||
# You can comment in/out various versions below
|
||||
#
|
||||
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||
# used with pair_style reaxff, provided that the QEq parameters are the same.
|
||||
#
|
||||
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||
# the QEq parameters are the same. These two styles can also be used with
|
||||
# pair_style reaxff.
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.CHO
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff NULL checkqeq no
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
group type1 type 1
|
||||
60 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
group type2 type 2
|
||||
25 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
group type3 type 3
|
||||
20 atoms in group type3
|
||||
compute charge3 type3 property/atom q
|
||||
compute q3 type3 reduce ave c_charge3
|
||||
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
||||
|
||||
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
||||
thermo 1
|
||||
|
||||
velocity all create 300.0 1281937
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
||||
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
||||
|
||||
timestep 0.25
|
||||
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.54 | 14.54 | 14.54 Mbytes
|
||||
Step PotEng c_q1 c_q2 c_q3 v_qtot
|
||||
0 -10226.557 0.095633909 -0.15658753 -0.091167311 -2.8865799e-15
|
||||
1 -10225.799 0.095650157 -0.15662321 -0.091171465 5.3290705e-15
|
||||
2 -10223.656 0.095669727 -0.15666713 -0.091175264 -2.8865799e-15
|
||||
3 -10220.276 0.095691262 -0.15671593 -0.09117887 4.6629367e-15
|
||||
4 -10215.894 0.095714037 -0.15676816 -0.091181914 4.4408921e-16
|
||||
5 -10210.804 0.095733939 -0.15681378 -0.091184589 -3.9968029e-15
|
||||
6 -10205.342 0.09575102 -0.15685378 -0.091185835 -3.5527137e-15
|
||||
7 -10199.848 0.095762356 -0.1568802 -0.091186815 2.220446e-15
|
||||
8 -10194.646 0.095766731 -0.15689071 -0.091186805 -3.9968029e-15
|
||||
9 -10190.016 0.095761083 -0.15687817 -0.091185537 -2.6645353e-15
|
||||
10 -10186.168 0.095747444 -0.15684695 -0.091183644 -1.5543122e-15
|
||||
Loop time of 0.013327 on 1 procs for 10 steps with 105 atoms
|
||||
|
||||
Performance: 16.208 ns/day, 1.481 hours/ns, 750.359 timesteps/s, 78.788 katom-step/s
|
||||
97.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.010565 | 0.010565 | 0.010565 | 0.0 | 79.28
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.3272e-05 | 2.3272e-05 | 2.3272e-05 | 0.0 | 0.17
|
||||
Output | 0.00023198 | 0.00023198 | 0.00023198 | 0.0 | 1.74
|
||||
Modify | 0.0024913 | 0.0024913 | 0.0024913 | 0.0 | 18.69
|
||||
Other | | 1.529e-05 | | | 0.11
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3417 ave 3417 max 3417 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3417
|
||||
Ave neighs/atom = 32.542857
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
146
examples/qeq/log.30Nov23.reaxff.g++.4
Normal file
146
examples/qeq/log.30Nov23.reaxff.g++.4
Normal file
@ -0,0 +1,146 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# This example demonstrates the use of various fix qeq variants with pair reaxff
|
||||
# You can comment in/out various versions below
|
||||
#
|
||||
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
||||
# used with pair_style reaxff, provided that the QEq parameters are the same.
|
||||
#
|
||||
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
||||
# the QEq parameters are the same. These two styles can also be used with
|
||||
# pair_style reaxff.
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
|
||||
read_data data.CHO
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style reaxff NULL checkqeq no
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
group type1 type 1
|
||||
60 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
group type2 type 2
|
||||
25 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
group type3 type 3
|
||||
20 atoms in group type3
|
||||
compute charge3 type3 property/atom q
|
||||
compute q3 type3 reduce ave c_charge3
|
||||
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
||||
|
||||
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
||||
thermo 1
|
||||
|
||||
velocity all create 300.0 1281937
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
||||
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
||||
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
||||
|
||||
timestep 0.25
|
||||
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.845 | 10.57 | 11.28 Mbytes
|
||||
Step PotEng c_q1 c_q2 c_q3 v_qtot
|
||||
0 -10226.557 0.095633904 -0.15658758 -0.091167237 -8.8817842e-16
|
||||
1 -10225.799 0.095650278 -0.1566235 -0.091171458 -1.7763568e-15
|
||||
2 -10223.656 0.095669806 -0.15666728 -0.091175321 0
|
||||
3 -10220.276 0.095691215 -0.15671588 -0.091178792 1.7763568e-15
|
||||
4 -10215.894 0.09571392 -0.15676795 -0.091181826 1.7763568e-15
|
||||
5 -10210.804 0.095734058 -0.15681436 -0.091184227 1.3322676e-15
|
||||
6 -10205.342 0.095751113 -0.15685409 -0.091185731 -4.4408921e-16
|
||||
7 -10199.848 0.095762524 -0.15688062 -0.091186803 -1.3322676e-15
|
||||
8 -10194.646 0.095766647 -0.15689045 -0.091186875 2.8865799e-15
|
||||
9 -10190.016 0.095760978 -0.15687772 -0.09118579 -4.4408921e-16
|
||||
10 -10186.168 0.095747037 -0.15684594 -0.091183687 -1.5543122e-15
|
||||
Loop time of 0.00732332 on 4 procs for 10 steps with 105 atoms
|
||||
|
||||
Performance: 29.495 ns/day, 0.814 hours/ns, 1365.500 timesteps/s, 143.378 katom-step/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0033186 | 0.0038166 | 0.0041063 | 0.5 | 52.12
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0002671 | 0.00057126 | 0.0010608 | 0.0 | 7.80
|
||||
Output | 0.00019157 | 0.0002237 | 0.00028058 | 0.0 | 3.05
|
||||
Modify | 0.0026446 | 0.0026528 | 0.0026604 | 0.0 | 36.22
|
||||
Other | | 5.9e-05 | | | 0.81
|
||||
|
||||
Nlocal: 26.25 ave 35 max 15 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 300 ave 357 max 239 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1025.25 ave 1468 max 405 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 4101
|
||||
Ave neighs/atom = 39.057143
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,23 +1,23 @@
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
run 3000
|
||||
run 2000
|
||||
|
||||
@ -1,17 +1,8 @@
|
||||
simulation_name AB_example ! output files will carry this name + their specific ext
|
||||
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
energy_update_freq 1
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
write_freq 1 ! write trajectory after so many steps
|
||||
traj_title AB ! (no white spaces)
|
||||
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
|
||||
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
|
||||
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
|
||||
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
|
||||
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
|
||||
|
||||
131
examples/reaxff/AB/log.30Nov23.AB.g++.1
Normal file
131
examples/reaxff/AB/log.30Nov23.AB.g++.1
Normal file
@ -0,0 +1,131 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
104 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
Reading potential file ffield.reax.AB with DATE: 2011-02-18
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
run 2000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.54 | 16.54 | 16.54 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8505.1816 0 -8505.1816 -673.36566
|
||||
100 83.873108 -8497.003 0 -8471.252 -609.71138
|
||||
200 125.22992 -8479.8879 0 -8441.4394 -1069.4072
|
||||
300 202.34273 -8479.1321 0 -8417.0081 -707.7946
|
||||
400 260.53055 -8476.7914 0 -8396.8025 221.10403
|
||||
500 282.47043 -8466.8576 0 -8380.1326 -223.61988
|
||||
600 288.72043 -8452.9503 0 -8364.3064 681.87761
|
||||
700 379.03381 -8467.4869 0 -8351.1146 921.82426
|
||||
800 382.0856 -8458.717 0 -8341.4078 253.69164
|
||||
900 380.10802 -8449.5745 0 -8332.8725 1199.5539
|
||||
1000 377.60669 -8440.3419 0 -8324.4078 -365.02585
|
||||
1100 372.89451 -8428.8743 0 -8314.387 -1401.9593
|
||||
1200 392.77958 -8426.3492 0 -8305.7567 -572.78319
|
||||
1300 429.04209 -8430.6839 0 -8298.958 -409.55236
|
||||
1400 471.52489 -8438.2785 0 -8293.5093 -16.649651
|
||||
1500 404.49399 -8411.1192 0 -8286.93 338.99191
|
||||
1600 443.77567 -8418.1237 0 -8281.8741 -774.22575
|
||||
1700 479.8234 -8424.6901 0 -8277.3731 65.260334
|
||||
1800 386.73299 -8390.8969 0 -8272.1608 70.076616
|
||||
1900 431.57275 -8401.0671 0 -8268.5641 30.882406
|
||||
2000 454.96043 -8406.0467 0 -8266.3632 728.1499
|
||||
Loop time of 2.35094 on 1 procs for 2000 steps with 104 atoms
|
||||
|
||||
Performance: 18.376 ns/day, 1.306 hours/ns, 850.725 timesteps/s, 88.475 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.9254 | 1.9254 | 1.9254 | 0.0 | 81.90
|
||||
Neigh | 0.10479 | 0.10479 | 0.10479 | 0.0 | 4.46
|
||||
Comm | 0.0067523 | 0.0067523 | 0.0067523 | 0.0 | 0.29
|
||||
Output | 0.0005375 | 0.0005375 | 0.0005375 | 0.0 | 0.02
|
||||
Modify | 0.31152 | 0.31152 | 0.31152 | 0.0 | 13.25
|
||||
Other | | 0.001934 | | | 0.08
|
||||
|
||||
Nlocal: 104 ave 104 max 104 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 710 ave 710 max 710 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3076 ave 3076 max 3076 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3076
|
||||
Ave neighs/atom = 29.576923
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
131
examples/reaxff/AB/log.30Nov23.AB.g++.4
Normal file
131
examples/reaxff/AB/log.30Nov23.AB.g++.4
Normal file
@ -0,0 +1,131 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
104 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
Reading potential file ffield.reax.AB with DATE: 2011-02-18
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
run 2000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.06 | 11.68 | 11.96 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8505.1816 0 -8505.1816 -673.36566
|
||||
100 83.873123 -8497.0031 0 -8471.252 -609.71119
|
||||
200 125.23001 -8479.8879 0 -8441.4394 -1069.4122
|
||||
300 202.34219 -8479.1319 0 -8417.0081 -707.82246
|
||||
400 260.52726 -8476.7906 0 -8396.8026 221.14446
|
||||
500 282.4624 -8466.8556 0 -8380.133 -223.17501
|
||||
600 288.8059 -8452.9729 0 -8364.3028 679.38441
|
||||
700 378.87007 -8467.429 0 -8351.107 920.99401
|
||||
800 382.10004 -8458.7194 0 -8341.4058 256.06383
|
||||
900 379.69698 -8449.4416 0 -8332.8657 1266.1715
|
||||
1000 379.63496 -8440.9584 0 -8324.4015 -604.987
|
||||
1100 372.82256 -8428.7507 0 -8314.2854 -1236.8451
|
||||
1200 397.12809 -8427.4286 0 -8305.501 -356.42394
|
||||
1300 413.36951 -8425.3861 0 -8298.472 -47.619729
|
||||
1400 428.68835 -8424.4328 0 -8292.8154 -812.52975
|
||||
1500 403.59408 -8411.0829 0 -8287.1701 71.054401
|
||||
1600 448.76276 -8419.8186 0 -8282.0379 -339.19148
|
||||
1700 450.87444 -8416.1981 0 -8277.769 -44.043208
|
||||
1800 485.33509 -8421.3776 0 -8272.3684 -848.94941
|
||||
1900 481.36374 -8416.1719 0 -8268.382 -282.62675
|
||||
2000 437.25967 -8398.9233 0 -8264.6743 -217.40762
|
||||
Loop time of 1.44368 on 4 procs for 2000 steps with 104 atoms
|
||||
|
||||
Performance: 29.924 ns/day, 0.802 hours/ns, 1385.350 timesteps/s, 144.076 katom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.77999 | 0.87212 | 0.96576 | 8.1 | 60.41
|
||||
Neigh | 0.054058 | 0.059726 | 0.06287 | 1.4 | 4.14
|
||||
Comm | 0.031767 | 0.12609 | 0.21802 | 21.3 | 8.73
|
||||
Output | 0.00041377 | 0.00045661 | 0.00058001 | 0.0 | 0.03
|
||||
Modify | 0.3805 | 0.38348 | 0.3894 | 0.6 | 26.56
|
||||
Other | | 0.001808 | | | 0.13
|
||||
|
||||
Nlocal: 26 ave 34 max 14 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 429.25 ave 457 max 386 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 922.5 ave 1238 max 496 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3690
|
||||
Ave neighs/atom = 35.480769
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
104 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
Reading potential file ffield.reax.AB with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.3 | 19.3 | 19.3 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8505.1816 0 -8505.1816 -673.36566
|
||||
3000 478.18595 -8398.4168 0 -8251.6025 1452.6935
|
||||
Loop time of 14.3573 on 1 procs for 3000 steps with 104 atoms
|
||||
|
||||
Performance: 4.513 ns/day, 5.318 hours/ns, 208.952 timesteps/s
|
||||
96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.709 | 12.709 | 12.709 | 0.0 | 88.52
|
||||
Neigh | 0.36804 | 0.36804 | 0.36804 | 0.0 | 2.56
|
||||
Comm | 0.022419 | 0.022419 | 0.022419 | 0.0 | 0.16
|
||||
Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.00
|
||||
Modify | 1.2513 | 1.2513 | 1.2513 | 0.0 | 8.72
|
||||
Other | | 0.006263 | | | 0.04
|
||||
|
||||
Nlocal: 104 ave 104 max 104 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 694 ave 694 max 694 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2866 ave 2866 max 2866 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2866
|
||||
Ave neighs/atom = 27.5577
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:14
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
104 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
Reading potential file ffield.reax.AB with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.38 | 13.22 | 13.64 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8505.1816 0 -8505.1816 -673.36566
|
||||
3000 555.17702 -8426.5541 0 -8256.1017 219.26856
|
||||
Loop time of 9.03521 on 4 procs for 3000 steps with 104 atoms
|
||||
|
||||
Performance: 7.172 ns/day, 3.346 hours/ns, 332.034 timesteps/s
|
||||
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.0347 | 7.0652 | 7.1049 | 1.0 | 78.20
|
||||
Neigh | 0.18481 | 0.20727 | 0.22108 | 3.0 | 2.29
|
||||
Comm | 0.075175 | 0.11496 | 0.14517 | 7.4 | 1.27
|
||||
Output | 2.2888e-05 | 2.569e-05 | 3.1948e-05 | 0.0 | 0.00
|
||||
Modify | 1.6286 | 1.6421 | 1.6649 | 1.1 | 18.17
|
||||
Other | | 0.005646 | | | 0.06
|
||||
|
||||
Nlocal: 26 ave 35 max 13 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Nghost: 420.25 ave 454 max 370 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 862.5 ave 1178 max 444 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3450
|
||||
Ave neighs/atom = 33.1731
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:09
|
||||
@ -1,23 +1,25 @@
|
||||
# REAX potential for AuO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
thermo 5
|
||||
|
||||
run 100
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
|
||||
run 100
|
||||
|
||||
@ -1,17 +1,7 @@
|
||||
simulation_name AuO_example ! output files will carry this name + their specific ext
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
energy_update_freq 1
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
write_freq 1 ! write trajectory after so many steps
|
||||
traj_title AuO ! (no white spaces)
|
||||
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
|
||||
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
|
||||
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
|
||||
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
|
||||
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
|
||||
|
||||
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.1
Normal file
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.1
Normal file
@ -0,0 +1,132 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for AuO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (26.15618 21.54252 24.00246)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
960 atoms
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
thermo 5
|
||||
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 4 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 129.2 | 129.2 | 129.2 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -72201.743 0 -72201.743 -166.19508
|
||||
5 6.5398577 -72202.679 0 -72183.984 71.658901
|
||||
10 13.280881 -72204.445 0 -72166.481 515.28836
|
||||
15 19.951637 -72206.24 0 -72149.206 886.438
|
||||
20 26.441301 -72207.78 0 -72132.195 1549.914
|
||||
25 32.580167 -72208.5 0 -72115.367 2309.8004
|
||||
30 38.264935 -72208.14 0 -72098.756 3148.7379
|
||||
35 43.433009 -72206.523 0 -72082.366 3853.4389
|
||||
40 48.028176 -72203.472 0 -72066.178 4830.1846
|
||||
45 52.019459 -72198.85 0 -72050.147 5881.5166
|
||||
50 55.407353 -72192.638 0 -72034.251 6996.89
|
||||
55 58.218407 -72184.89 0 -72018.467 8191.8057
|
||||
60 60.499102 -72175.717 0 -72002.774 9470.0601
|
||||
65 62.309031 -72165.271 0 -71987.155 10831.309
|
||||
70 63.72857 -72153.749 0 -71971.575 12270.345
|
||||
75 64.847533 -72141.43 0 -71956.057 13791.775
|
||||
80 65.755809 -72128.548 0 -71940.579 15397.406
|
||||
85 66.547696 -72115.362 0 -71925.129 17100.883
|
||||
90 67.309412 -72102.119 0 -71909.708 18888.699
|
||||
95 68.120206 -72089.043 0 -71894.315 20757.038
|
||||
100 69.043359 -72076.31 0 -71878.942 22702.463
|
||||
Loop time of 5.72003 on 1 procs for 100 steps with 960 atoms
|
||||
|
||||
Performance: 0.378 ns/day, 63.556 hours/ns, 17.482 timesteps/s, 16.783 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.2903 | 4.2903 | 4.2903 | 0.0 | 75.00
|
||||
Neigh | 0.31194 | 0.31194 | 0.31194 | 0.0 | 5.45
|
||||
Comm | 0.0034139 | 0.0034139 | 0.0034139 | 0.0 | 0.06
|
||||
Output | 0.0005041 | 0.0005041 | 0.0005041 | 0.0 | 0.01
|
||||
Modify | 1.1134 | 1.1134 | 1.1134 | 0.0 | 19.46
|
||||
Other | | 0.0005147 | | | 0.01
|
||||
|
||||
Nlocal: 960 ave 960 max 960 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6708 ave 6708 max 6708 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 369128 ave 369128 max 369128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 369128
|
||||
Ave neighs/atom = 384.50833
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:05
|
||||
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.4
Normal file
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.4
Normal file
@ -0,0 +1,132 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for AuO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (26.15618 21.54252 24.00246)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
960 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
thermo 5
|
||||
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 4 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 71.65 | 71.65 | 71.65 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -72201.743 0 -72201.743 -166.19214
|
||||
5 6.5398578 -72202.679 0 -72183.984 71.651708
|
||||
10 13.280883 -72204.445 0 -72166.481 515.29601
|
||||
15 19.951639 -72206.24 0 -72149.206 886.53083
|
||||
20 26.441291 -72207.78 0 -72132.195 1550.0745
|
||||
25 32.580153 -72208.5 0 -72115.366 2309.9393
|
||||
30 38.264928 -72208.14 0 -72098.756 3148.6036
|
||||
35 43.432999 -72206.523 0 -72082.365 3853.6963
|
||||
40 48.028158 -72203.472 0 -72066.179 4830.1407
|
||||
45 52.019436 -72198.85 0 -72050.147 5881.1916
|
||||
50 55.407331 -72192.638 0 -72034.251 6996.6661
|
||||
55 58.218406 -72184.89 0 -72018.467 8191.9075
|
||||
60 60.499115 -72175.716 0 -72002.774 9470.4845
|
||||
65 62.309058 -72165.271 0 -71987.154 10831.926
|
||||
70 63.728581 -72153.75 0 -71971.575 12269.823
|
||||
75 64.847544 -72141.431 0 -71956.058 13791.586
|
||||
80 65.755816 -72128.549 0 -71940.579 15396.822
|
||||
85 66.547694 -72115.363 0 -71925.13 17100.27
|
||||
90 67.309401 -72102.119 0 -71909.708 18888.633
|
||||
95 68.120175 -72089.042 0 -71894.314 20757.565
|
||||
100 69.043333 -72076.31 0 -71878.943 22701.953
|
||||
Loop time of 2.52972 on 4 procs for 100 steps with 960 atoms
|
||||
|
||||
Performance: 0.854 ns/day, 28.108 hours/ns, 39.530 timesteps/s, 37.949 katom-step/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.9911 | 2.0015 | 2.0084 | 0.5 | 79.12
|
||||
Neigh | 0.16044 | 0.16105 | 0.16228 | 0.2 | 6.37
|
||||
Comm | 0.018211 | 0.025417 | 0.03612 | 4.2 | 1.00
|
||||
Output | 0.00039837 | 0.00043613 | 0.00054664 | 0.0 | 0.02
|
||||
Modify | 0.34008 | 0.34101 | 0.34154 | 0.1 | 13.48
|
||||
Other | | 0.0003489 | | | 0.01
|
||||
|
||||
Nlocal: 240 ave 240 max 240 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3981 ave 3981 max 3981 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105979 ave 105979 max 105979 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 423916
|
||||
Ave neighs/atom = 441.57917
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for AuO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
960 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 4 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 157.6 | 157.6 | 157.6 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -72201.743 0 -72201.743 -166.19482
|
||||
100 69.043331 -72076.309 0 -71878.942 22702.89
|
||||
Loop time of 18.4369 on 1 procs for 100 steps with 960 atoms
|
||||
|
||||
Performance: 0.117 ns/day, 204.854 hours/ns, 5.424 timesteps/s
|
||||
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 15.373 | 15.373 | 15.373 | 0.0 | 83.38
|
||||
Neigh | 0.58774 | 0.58774 | 0.58774 | 0.0 | 3.19
|
||||
Comm | 0.0079026 | 0.0079026 | 0.0079026 | 0.0 | 0.04
|
||||
Output | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00
|
||||
Modify | 2.4665 | 2.4665 | 2.4665 | 0.0 | 13.38
|
||||
Other | | 0.001366 | | | 0.01
|
||||
|
||||
Nlocal: 960 ave 960 max 960 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6708 ave 6708 max 6708 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 369128 ave 369128 max 369128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 369128
|
||||
Ave neighs/atom = 384.508
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:18
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for AuO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
960 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
Reading potential file ffield.reax.AuO with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 4 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 87.17 | 87.17 | 87.17 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -72201.743 0 -72201.743 -166.2027
|
||||
100 69.043379 -72076.31 0 -71878.943 22701.771
|
||||
Loop time of 8.44797 on 4 procs for 100 steps with 960 atoms
|
||||
|
||||
Performance: 0.256 ns/day, 93.866 hours/ns, 11.837 timesteps/s
|
||||
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.3702 | 7.3757 | 7.3879 | 0.3 | 87.31
|
||||
Neigh | 0.28875 | 0.29449 | 0.29747 | 0.6 | 3.49
|
||||
Comm | 0.015008 | 0.027055 | 0.032681 | 4.3 | 0.32
|
||||
Output | 2.4319e-05 | 2.8551e-05 | 3.8624e-05 | 0.0 | 0.00
|
||||
Modify | 0.74721 | 0.74985 | 0.75539 | 0.4 | 8.88
|
||||
Other | | 0.0008975 | | | 0.01
|
||||
|
||||
Nlocal: 240 ave 240 max 240 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3981 ave 3981 max 3981 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105979 ave 105979 max 105979 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 423916
|
||||
Ave neighs/atom = 441.579
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:08
|
||||
@ -1,23 +1,24 @@
|
||||
# REAX potential for CHO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
|
||||
run 3000
|
||||
run 3000
|
||||
|
||||
@ -1,17 +1,8 @@
|
||||
simulation_name CHO_example ! output files will carry this name + their specific ext
|
||||
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
energy_update_freq 1
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
write_freq 1 ! write trajectory after so many steps
|
||||
traj_title CHO ! (no white spaces)
|
||||
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
|
||||
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
|
||||
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
|
||||
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
|
||||
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
|
||||
|
||||
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.1
Normal file
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.1
Normal file
@ -0,0 +1,141 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for CHO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.04 | 16.04 | 16.04 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10226.557 0 -10226.557 -106.09742
|
||||
100 54.051992 -10207.393 0 -10190.636 -291.38729
|
||||
200 134.81151 -10200.411 0 -10158.619 -1637.1719
|
||||
300 140.9118 -10177.136 0 -10133.452 -1668.5701
|
||||
400 254.70109 -10189.927 0 -10110.969 -2522.3829
|
||||
500 228.22383 -10162.396 0 -10091.646 404.00518
|
||||
600 393.48635 -10197.284 0 -10075.301 394.0729
|
||||
700 305.82675 -10156.708 0 -10061.9 362.69731
|
||||
800 375.9566 -10170.288 0 -10053.74 -664.01093
|
||||
900 361.59639 -10155.849 0 -10043.752 458.54613
|
||||
1000 445.46183 -10176.602 0 -10038.507 251.38181
|
||||
1100 475.46673 -10180.119 0 -10032.723 839.6649
|
||||
1200 406.78262 -10155.498 0 -10029.394 62.559824
|
||||
1300 461.0773 -10167.129 0 -10024.193 266.27742
|
||||
1400 408.15446 -10148.62 0 -10022.091 -1187.1776
|
||||
1500 514.43707 -10178.34 0 -10018.863 -616.2329
|
||||
1600 432.19202 -10151.16 0 -10017.179 -677.67834
|
||||
1700 521.01474 -10175.583 0 -10014.066 97.420991
|
||||
1800 409.79407 -10138.825 0 -10011.787 1883.8131
|
||||
1900 481.84667 -10160.146 0 -10010.772 1059.6448
|
||||
2000 423.61284 -10138.538 0 -10007.216 -434.24008
|
||||
2100 521.01756 -10169.192 0 -10007.674 376.95207
|
||||
2200 477.03314 -10153.033 0 -10005.151 -114.09514
|
||||
2300 477.80526 -10153.294 0 -10005.172 869.97281
|
||||
2400 471.49741 -10149.165 0 -10002.999 689.65295
|
||||
2500 482.38958 -10152.956 0 -10003.413 352.08649
|
||||
2600 505.57503 -10159.507 0 -10002.777 -812.75272
|
||||
2700 498.41415 -10156.448 0 -10001.937 -458.03311
|
||||
2800 534.65278 -10166.893 0 -10001.149 169.20767
|
||||
2900 432.93717 -10134.759 0 -10000.546 -184.75627
|
||||
3000 548.46832 -10170.375 0 -10000.347 41.765546
|
||||
Loop time of 3.49376 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 18.547 ns/day, 1.294 hours/ns, 858.673 timesteps/s, 90.161 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.8082 | 2.8082 | 2.8082 | 0.0 | 80.38
|
||||
Neigh | 0.15477 | 0.15477 | 0.15477 | 0.0 | 4.43
|
||||
Comm | 0.0097478 | 0.0097478 | 0.0097478 | 0.0 | 0.28
|
||||
Output | 0.00081006 | 0.00081006 | 0.00081006 | 0.0 | 0.02
|
||||
Modify | 0.51773 | 0.51773 | 0.51773 | 0.0 | 14.82
|
||||
Other | | 0.002538 | | | 0.07
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 643 ave 643 max 643 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4237 ave 4237 max 4237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4237
|
||||
Ave neighs/atom = 40.352381
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:03
|
||||
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.4
Normal file
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.4
Normal file
@ -0,0 +1,141 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for CHO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.47 | 11.39 | 12.19 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10226.557 0 -10226.557 -106.09736
|
||||
100 54.051902 -10207.393 0 -10190.636 -291.39467
|
||||
200 134.81172 -10200.411 0 -10158.619 -1637.1599
|
||||
300 140.91215 -10177.136 0 -10133.452 -1668.5676
|
||||
400 254.70123 -10189.927 0 -10110.968 -2522.3655
|
||||
500 228.22204 -10162.396 0 -10091.646 403.98879
|
||||
600 393.48756 -10197.284 0 -10075.301 394.11243
|
||||
700 305.82625 -10156.707 0 -10061.9 362.73212
|
||||
800 375.95634 -10170.288 0 -10053.74 -664.10079
|
||||
900 361.59143 -10155.847 0 -10043.752 458.52018
|
||||
1000 445.4582 -10176.601 0 -10038.507 251.4509
|
||||
1100 475.47 -10180.12 0 -10032.722 840.09331
|
||||
1200 406.77476 -10155.496 0 -10029.394 62.656622
|
||||
1300 461.06079 -10167.123 0 -10024.192 265.91062
|
||||
1400 408.15869 -10148.621 0 -10022.09 -1187.4869
|
||||
1500 514.43021 -10178.337 0 -10018.862 -616.07216
|
||||
1600 432.22013 -10151.168 0 -10017.178 -678.01121
|
||||
1700 521.0846 -10175.605 0 -10014.067 98.591699
|
||||
1800 409.72383 -10138.803 0 -10011.787 1884.7989
|
||||
1900 481.86369 -10160.152 0 -10010.773 1058.5554
|
||||
2000 423.60058 -10138.532 0 -10007.214 -437.22408
|
||||
2100 520.96555 -10169.169 0 -10007.668 376.18619
|
||||
2200 477.21351 -10153.089 0 -10005.15 -113.43512
|
||||
2300 477.86263 -10153.309 0 -10005.17 868.89369
|
||||
2400 471.46466 -10149.152 0 -10002.996 688.76379
|
||||
2500 482.61616 -10153.025 0 -10003.412 350.03715
|
||||
2600 505.68439 -10159.544 0 -10002.78 -810.94974
|
||||
2700 498.37307 -10156.441 0 -10001.944 -460.12105
|
||||
2800 535.06218 -10167.029 0 -10001.157 152.85379
|
||||
2900 432.98591 -10134.778 0 -10000.55 -170.46638
|
||||
3000 547.92956 -10170.199 0 -10000.339 60.201766
|
||||
Loop time of 2.03179 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 31.893 ns/day, 0.753 hours/ns, 1476.533 timesteps/s, 155.036 katom-step/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.213 | 1.2396 | 1.2505 | 1.4 | 61.01
|
||||
Neigh | 0.074765 | 0.08966 | 0.10323 | 4.3 | 4.41
|
||||
Comm | 0.12894 | 0.14116 | 0.16833 | 4.2 | 6.95
|
||||
Output | 0.0006079 | 0.00066664 | 0.00083802 | 0.0 | 0.03
|
||||
Modify | 0.54589 | 0.55836 | 0.57217 | 1.6 | 27.48
|
||||
Other | | 0.002368 | | | 0.12
|
||||
|
||||
Nlocal: 26.25 ave 45 max 6 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 380.75 ave 495 max 261 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 1269.5 ave 2197 max 179 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 5078
|
||||
Ave neighs/atom = 48.361905
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for CHO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10226.557 0 -10226.557 -106.09755
|
||||
3000 548.5116 -10170.389 0 -10000.348 40.372297
|
||||
Loop time of 12.6046 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 5.141 ns/day, 4.668 hours/ns, 238.008 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.931 | 10.931 | 10.931 | 0.0 | 86.72
|
||||
Neigh | 0.33107 | 0.33107 | 0.33107 | 0.0 | 2.63
|
||||
Comm | 0.017975 | 0.017975 | 0.017975 | 0.0 | 0.14
|
||||
Output | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 | 0.0 | 0.00
|
||||
Modify | 1.3197 | 1.3197 | 1.3197 | 0.0 | 10.47
|
||||
Other | | 0.005059 | | | 0.04
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 643 ave 643 max 643 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4237 ave 4237 max 4237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4237
|
||||
Ave neighs/atom = 40.3524
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:12
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for CHO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.75 | 12.85 | 13.81 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10226.557 0 -10226.557 -106.09745
|
||||
3000 548.30567 -10170.323 0 -10000.346 47.794514
|
||||
Loop time of 7.42367 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 8.729 ns/day, 2.750 hours/ns, 404.113 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.3058 | 5.4086 | 5.4922 | 3.1 | 72.86
|
||||
Neigh | 0.14791 | 0.17866 | 0.2106 | 6.5 | 2.41
|
||||
Comm | 0.080185 | 0.16666 | 0.26933 | 17.7 | 2.24
|
||||
Output | 2.5988e-05 | 2.8491e-05 | 3.4571e-05 | 0.0 | 0.00
|
||||
Modify | 1.6364 | 1.6658 | 1.6941 | 2.0 | 22.44
|
||||
Other | | 0.003964 | | | 0.05
|
||||
|
||||
Nlocal: 26.25 ave 45 max 6 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 380.75 ave 495 max 261 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 1269.5 ave 2197 max 179 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 5078
|
||||
Ave neighs/atom = 48.3619
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -3,33 +3,33 @@
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||
|
||||
# should equilibrate much longer in practice
|
||||
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
timestep 0.2
|
||||
thermo_style custom step temp epair etotal press
|
||||
thermo 1
|
||||
dump 4 all xyz 5000 dumpnpt.xyz
|
||||
run 10
|
||||
run 10
|
||||
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt temp 100.0 100.0 100.0
|
||||
thermo_style custom step temp epair etotal press
|
||||
timestep 0.2
|
||||
timestep 0.2
|
||||
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||
|
||||
run 10
|
||||
run 10
|
||||
|
||||
172
examples/reaxff/FC/log.30Nov23.FC.g++.1
Normal file
172
examples/reaxff/FC/log.30Nov23.FC.g++.1
Normal file
@ -0,0 +1,172 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
Reading data file ...
|
||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
17280 atoms
|
||||
read_data CPU = 0.025 seconds
|
||||
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||
|
||||
# should equilibrate much longer in practice
|
||||
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
timestep 0.2
|
||||
thermo_style custom step temp epair etotal press
|
||||
thermo 1
|
||||
dump 4 all xyz 5000 dumpnpt.xyz
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 28 27 17
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 384.3 | 384.3 | 384.3 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
0 0 -808525.04 -808525.04 58194.694
|
||||
1 4.9935726 -808803.88 -808546.69 58205.825
|
||||
2 19.98696 -809640.53 -808611.1 58239.155
|
||||
3 45.012616 -811035.3 -808716.9 58294.499
|
||||
4 80.103613 -812988.58 -808862.81 58371.548
|
||||
5 125.26228 -815500.68 -809049 58469.872
|
||||
6 180.4316 -818571.56 -809278.36 58588.936
|
||||
7 245.47913 -822200.73 -809557.22 58728.144
|
||||
8 320.17692 -826387.19 -809896.34 58886.879
|
||||
9 404.17073 -831129.38 -810312.4 59064.554
|
||||
10 497.02486 -836425.06 -810825.59 59260.717
|
||||
Loop time of 6.13793 on 1 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.028 ns/day, 852.491 hours/ns, 1.629 timesteps/s, 28.153 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1752 | 5.1752 | 5.1752 | 0.0 | 84.31
|
||||
Neigh | 0.039453 | 0.039453 | 0.039453 | 0.0 | 0.64
|
||||
Comm | 0.00042596 | 0.00042596 | 0.00042596 | 0.0 | 0.01
|
||||
Output | 0.00064013 | 0.00064013 | 0.00064013 | 0.0 | 0.01
|
||||
Modify | 0.92205 | 0.92205 | 0.92205 | 0.0 | 15.02
|
||||
Other | | 0.0002045 | | | 0.00
|
||||
|
||||
Nlocal: 17280 ave 17280 max 17280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5352 ave 5352 max 5352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2621360
|
||||
Ave neighs/atom = 151.69907
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt temp 100.0 100.0 100.0
|
||||
thermo_style custom step temp epair etotal press
|
||||
timestep 0.2
|
||||
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||
|
||||
run 10
|
||||
Per MPI rank memory allocation (min/avg/max) = 386.9 | 386.9 | 386.9 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
10 497.02486 -836425.06 -810825.59 59260.717
|
||||
11 601.6514 -841814.09 -810825.78 59489.425
|
||||
12 716.37597 -847724.6 -810827.35 59738.298
|
||||
13 841.27959 -854161.62 -810831.16 60008.164
|
||||
14 976.4666 -861131.68 -810838.36 60300.364
|
||||
15 1122.0668 -868642.96 -810850.45 60616.793
|
||||
16 1278.2373 -876705.43 -810869.28 60959.942
|
||||
17 1445.1655 -885331.03 -810897.18 61332.932
|
||||
18 1623.072 -894533.91 -810936.92 61739.541
|
||||
19 1812.1864 -904337.86 -811000.45 62200.561
|
||||
20 2011.5898 -915379.05 -811771.28 63361.15
|
||||
Loop time of 6.11372 on 1 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.028 ns/day, 849.127 hours/ns, 1.636 timesteps/s, 28.264 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.0783 | 5.0783 | 5.0783 | 0.0 | 83.06
|
||||
Neigh | 0.03596 | 0.03596 | 0.03596 | 0.0 | 0.59
|
||||
Comm | 0.00041578 | 0.00041578 | 0.00041578 | 0.0 | 0.01
|
||||
Output | 0.00062133 | 0.00062133 | 0.00062133 | 0.0 | 0.01
|
||||
Modify | 0.99825 | 0.99825 | 0.99825 | 0.0 | 16.33
|
||||
Other | | 0.0002171 | | | 0.00
|
||||
|
||||
Nlocal: 17280 ave 17280 max 17280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5352 ave 5352 max 5352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2621360
|
||||
Ave neighs/atom = 151.69907
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:13
|
||||
172
examples/reaxff/FC/log.30Nov23.FC.g++.4
Normal file
172
examples/reaxff/FC/log.30Nov23.FC.g++.4
Normal file
@ -0,0 +1,172 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
Reading data file ...
|
||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
17280 atoms
|
||||
read_data CPU = 0.030 seconds
|
||||
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||
|
||||
# should equilibrate much longer in practice
|
||||
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
timestep 0.2
|
||||
thermo_style custom step temp epair etotal press
|
||||
thermo 1
|
||||
dump 4 all xyz 5000 dumpnpt.xyz
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 28 27 17
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 121.6 | 121.6 | 121.6 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
0 0 -808525.04 -808525.04 58194.694
|
||||
1 4.9935726 -808803.88 -808546.69 58205.825
|
||||
2 19.98696 -809640.53 -808611.1 58239.155
|
||||
3 45.012616 -811035.3 -808716.9 58294.499
|
||||
4 80.103613 -812988.58 -808862.81 58371.548
|
||||
5 125.26228 -815500.68 -809049 58469.872
|
||||
6 180.4316 -818571.56 -809278.36 58588.936
|
||||
7 245.47913 -822200.73 -809557.22 58728.144
|
||||
8 320.17692 -826387.19 -809896.34 58886.879
|
||||
9 404.17073 -831129.38 -810312.4 59064.554
|
||||
10 497.02486 -836425.06 -810825.59 59260.717
|
||||
Loop time of 1.75962 on 4 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.098 ns/day, 244.392 hours/ns, 5.683 timesteps/s, 98.203 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.402 | 1.4417 | 1.4815 | 3.0 | 81.93
|
||||
Neigh | 0.012815 | 0.013047 | 0.01323 | 0.2 | 0.74
|
||||
Comm | 0.0006609 | 0.040482 | 0.080149 | 17.9 | 2.30
|
||||
Output | 0.00028041 | 0.00029538 | 0.00033093 | 0.0 | 0.02
|
||||
Modify | 0.26389 | 0.26407 | 0.26425 | 0.0 | 15.01
|
||||
Other | | 7.451e-05 | | | 0.00
|
||||
|
||||
Nlocal: 4320 ave 4320 max 4320 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2856 ave 2856 max 2856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 691892 ave 691892 max 691892 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2767568
|
||||
Ave neighs/atom = 160.16019
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt temp 100.0 100.0 100.0
|
||||
thermo_style custom step temp epair etotal press
|
||||
timestep 0.2
|
||||
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||
|
||||
run 10
|
||||
Per MPI rank memory allocation (min/avg/max) = 123 | 123 | 123 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
10 497.02486 -836425.06 -810825.59 59260.717
|
||||
11 601.6514 -841814.09 -810825.78 59489.425
|
||||
12 716.37597 -847724.6 -810827.35 59738.298
|
||||
13 841.27959 -854161.62 -810831.16 60008.164
|
||||
14 976.4666 -861131.68 -810838.36 60300.364
|
||||
15 1122.0668 -868642.96 -810850.45 60616.793
|
||||
16 1278.2373 -876705.43 -810869.28 60959.942
|
||||
17 1445.1655 -885331.03 -810897.18 61332.932
|
||||
18 1623.072 -894533.91 -810936.92 61739.541
|
||||
19 1812.1864 -904337.86 -811000.45 62200.561
|
||||
20 2011.5898 -915379.05 -811771.28 63361.15
|
||||
Loop time of 1.8322 on 4 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.094 ns/day, 254.473 hours/ns, 5.458 timesteps/s, 94.313 katom-step/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3846 | 1.4468 | 1.524 | 4.2 | 78.96
|
||||
Neigh | 0.012048 | 0.012239 | 0.012522 | 0.2 | 0.67
|
||||
Comm | 0.00082283 | 0.07804 | 0.14024 | 17.9 | 4.26
|
||||
Output | 0.00029695 | 0.00031243 | 0.00035323 | 0.0 | 0.02
|
||||
Modify | 0.29449 | 0.29478 | 0.29497 | 0.0 | 16.09
|
||||
Other | | 7.342e-05 | | | 0.00
|
||||
|
||||
Nlocal: 4320 ave 4320 max 4320 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2856 ave 2856 max 2856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 691892 ave 691892 max 691892 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2767568
|
||||
Ave neighs/atom = 160.16019
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:04
|
||||
@ -1,141 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
17280 atoms
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
|
||||
# should equilibrate much longer in practice
|
||||
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
timestep 0.2
|
||||
thermo_style custom step temp epair etotal press
|
||||
thermo 1
|
||||
dump 4 all xyz 5000 dumpnpt.xyz
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 28 27 17
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
0 0 -808525.04 -808525.04 58194.694
|
||||
1 4.9935726 -808803.89 -808546.69 58205.825
|
||||
2 19.98696 -809640.54 -808611.1 58239.155
|
||||
3 45.012616 -811035.31 -808716.91 58294.499
|
||||
4 80.103613 -812988.6 -808862.83 58371.547
|
||||
5 125.26228 -815500.71 -809049.03 58469.871
|
||||
6 180.4316 -818571.61 -809278.4 58588.935
|
||||
7 245.47913 -822200.79 -809557.28 58728.142
|
||||
8 320.17692 -826387.27 -809896.43 58886.877
|
||||
9 404.17073 -831129.48 -810312.5 59064.551
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
Loop time of 21.5054 on 1 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.008 ns/day, 2986.857 hours/ns, 0.465 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.008 | 19.008 | 19.008 | 0.0 | 88.39
|
||||
Neigh | 0.084401 | 0.084401 | 0.084401 | 0.0 | 0.39
|
||||
Comm | 0.00080419 | 0.00080419 | 0.00080419 | 0.0 | 0.00
|
||||
Output | 0.00095367 | 0.00095367 | 0.00095367 | 0.0 | 0.00
|
||||
Modify | 2.4109 | 2.4109 | 2.4109 | 0.0 | 11.21
|
||||
Other | | 0.0004592 | | | 0.00
|
||||
|
||||
Nlocal: 17280 ave 17280 max 17280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5352 ave 5352 max 5352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2621360
|
||||
Ave neighs/atom = 151.699
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt temp 100.0 100.0 100.0
|
||||
thermo_style custom step temp epair etotal press
|
||||
timestep 0.2
|
||||
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||
|
||||
run 10
|
||||
Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
11 601.65141 -841814.22 -810825.91 59489.422
|
||||
12 716.37599 -847724.72 -810827.48 59738.295
|
||||
13 841.27961 -854161.75 -810831.29 60008.162
|
||||
14 976.46663 -861131.81 -810838.49 60300.362
|
||||
15 1122.0668 -868643.09 -810850.57 60616.791
|
||||
16 1278.2373 -876705.56 -810869.41 60959.94
|
||||
17 1445.1655 -885331.16 -810897.31 61332.931
|
||||
18 1623.072 -894534.04 -810937.04 61739.541
|
||||
19 1812.1865 -904337.99 -811000.57 62200.561
|
||||
20 2011.5899 -915379.19 -811771.41 63361.151
|
||||
Loop time of 21.362 on 1 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.008 ns/day, 2966.945 hours/ns, 0.468 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.793 | 18.793 | 18.793 | 0.0 | 87.97
|
||||
Neigh | 0.077047 | 0.077047 | 0.077047 | 0.0 | 0.36
|
||||
Comm | 0.00080276 | 0.00080276 | 0.00080276 | 0.0 | 0.00
|
||||
Output | 0.0010097 | 0.0010097 | 0.0010097 | 0.0 | 0.00
|
||||
Modify | 2.4897 | 2.4897 | 2.4897 | 0.0 | 11.65
|
||||
Other | | 0.0004568 | | | 0.00
|
||||
|
||||
Nlocal: 17280 ave 17280 max 17280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5352 ave 5352 max 5352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2621360
|
||||
Ave neighs/atom = 151.699
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:47
|
||||
@ -1,141 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
17280 atoms
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
|
||||
# should equilibrate much longer in practice
|
||||
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
timestep 0.2
|
||||
thermo_style custom step temp epair etotal press
|
||||
thermo 1
|
||||
dump 4 all xyz 5000 dumpnpt.xyz
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 28 27 17
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
0 0 -808525.04 -808525.04 58194.694
|
||||
1 4.9935726 -808803.89 -808546.69 58205.825
|
||||
2 19.98696 -809640.54 -808611.1 58239.155
|
||||
3 45.012616 -811035.31 -808716.91 58294.499
|
||||
4 80.103613 -812988.6 -808862.83 58371.547
|
||||
5 125.26228 -815500.71 -809049.03 58469.871
|
||||
6 180.4316 -818571.61 -809278.4 58588.935
|
||||
7 245.47913 -822200.79 -809557.28 58728.142
|
||||
8 320.17692 -826387.27 -809896.43 58886.877
|
||||
9 404.17073 -831129.48 -810312.5 59064.551
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
Loop time of 6.02109 on 4 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.029 ns/day, 836.262 hours/ns, 1.661 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.9482 | 5.1186 | 5.3113 | 7.4 | 85.01
|
||||
Neigh | 0.024811 | 0.025702 | 0.027556 | 0.7 | 0.43
|
||||
Comm | 0.0027421 | 0.19541 | 0.36565 | 38.1 | 3.25
|
||||
Output | 0.00053239 | 0.00057119 | 0.00067186 | 0.0 | 0.01
|
||||
Modify | 0.67876 | 0.68059 | 0.68165 | 0.1 | 11.30
|
||||
Other | | 0.0001779 | | | 0.00
|
||||
|
||||
Nlocal: 4320 ave 4320 max 4320 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2856 ave 2856 max 2856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 691892 ave 691892 max 691892 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2767568
|
||||
Ave neighs/atom = 160.16
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt temp 100.0 100.0 100.0
|
||||
thermo_style custom step temp epair etotal press
|
||||
timestep 0.2
|
||||
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||
|
||||
run 10
|
||||
Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
11 601.65141 -841814.22 -810825.91 59489.422
|
||||
12 716.37599 -847724.72 -810827.48 59738.295
|
||||
13 841.27961 -854161.75 -810831.29 60008.162
|
||||
14 976.46663 -861131.81 -810838.49 60300.362
|
||||
15 1122.0668 -868643.09 -810850.57 60616.791
|
||||
16 1278.2373 -876705.56 -810869.41 60959.94
|
||||
17 1445.1655 -885331.16 -810897.31 61332.931
|
||||
18 1623.072 -894534.04 -810937.04 61739.541
|
||||
19 1812.1865 -904337.99 -811000.57 62200.561
|
||||
20 2011.5899 -915379.19 -811771.41 63361.151
|
||||
Loop time of 6.08805 on 4 procs for 10 steps with 17280 atoms
|
||||
|
||||
Performance: 0.028 ns/day, 845.563 hours/ns, 1.643 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.9124 | 5.1008 | 5.3405 | 8.3 | 83.78
|
||||
Neigh | 0.023652 | 0.024473 | 0.025996 | 0.6 | 0.40
|
||||
Comm | 0.0020971 | 0.24171 | 0.43023 | 38.0 | 3.97
|
||||
Output | 0.00056076 | 0.00060701 | 0.00072312 | 0.0 | 0.01
|
||||
Modify | 0.71869 | 0.72023 | 0.72107 | 0.1 | 11.83
|
||||
Other | | 0.0001827 | | | 0.00
|
||||
|
||||
Nlocal: 4320 ave 4320 max 4320 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2856 ave 2856 max 2856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 691892 ave 691892 max 691892 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2767568
|
||||
Ave neighs/atom = 160.16
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:13
|
||||
@ -1,23 +1,24 @@
|
||||
# REAX potential for Fe/O/H system
|
||||
# .....
|
||||
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
|
||||
run 3000
|
||||
run 3000
|
||||
|
||||
@ -1,17 +1,7 @@
|
||||
simulation_name FeOH3_example ! output files will carry this name + their specific ext
|
||||
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
energy_update_freq 1
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
write_freq 1 ! write trajectory after so many steps
|
||||
traj_title Fe_OH3 ! (no white spaces)
|
||||
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
|
||||
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
|
||||
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
|
||||
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
|
||||
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1
Normal file
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1
Normal file
@ -0,0 +1,141 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Fe/O/H system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
Reading potential file ffield.reax.Fe_O_C_H with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.99 | 15.99 | 15.99 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||
100 127.38829 -9720.5854 0 -9681.0945 -933.74373
|
||||
200 141.21008 -9696.3143 0 -9652.5386 -831.74241
|
||||
300 176.81083 -9681.3376 0 -9626.5255 -520.30966
|
||||
400 220.75236 -9672.6196 0 -9604.1854 -388.85436
|
||||
500 301.29415 -9678.8463 0 -9585.4438 -545.22735
|
||||
600 320.36877 -9670.3054 0 -9570.9897 -609.44044
|
||||
700 414.53699 -9688.649 0 -9560.1408 -259.51791
|
||||
800 391.93073 -9675.1212 0 -9553.621 77.352757
|
||||
900 413.52476 -9673.7372 0 -9545.5428 369.71918
|
||||
1000 382.03337 -9656.3848 0 -9537.9528 236.61186
|
||||
1100 381.68223 -9647.4372 0 -9529.1141 -432.67374
|
||||
1200 470.68889 -9671.5116 0 -9525.596 448.90781
|
||||
1300 436.34973 -9659.2277 0 -9523.9574 188.12079
|
||||
1400 422.25034 -9651.2639 0 -9520.3645 48.988693
|
||||
1500 363.49223 -9625.6588 0 -9512.9746 -977.83513
|
||||
1600 450.39155 -9646.4742 0 -9506.8509 44.80204
|
||||
1700 461.44884 -9648.1215 0 -9505.0704 -29.381385
|
||||
1800 457.01538 -9644.6842 0 -9503.0075 -29.157643
|
||||
1900 461.56497 -9642.8457 0 -9499.7586 -608.58801
|
||||
2000 491.20199 -9648.6637 0 -9496.389 -99.409356
|
||||
2100 461.60295 -9636.4878 0 -9493.3889 753.00956
|
||||
2200 480.92601 -9640.304 0 -9491.2149 -176.4371
|
||||
2300 450.00958 -9627.8875 0 -9488.3826 -210.21397
|
||||
2400 475.97134 -9634.1577 0 -9486.6046 -364.46797
|
||||
2500 478.0174 -9631.5069 0 -9483.3194 557.79107
|
||||
2600 500.26141 -9636.8606 0 -9481.7774 115.84535
|
||||
2700 455.06433 -9620.0151 0 -9478.9433 -963.22
|
||||
2800 441.50799 -9612.6546 0 -9475.7852 -177.60856
|
||||
2900 471.67031 -9618.9817 0 -9472.7619 -294.38595
|
||||
3000 526.94336 -9635.8664 0 -9472.5117 119.05777
|
||||
Loop time of 2.33387 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 27.765 ns/day, 0.864 hours/ns, 1285.420 timesteps/s, 134.969 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.8409 | 1.8409 | 1.8409 | 0.0 | 78.88
|
||||
Neigh | 0.15998 | 0.15998 | 0.15998 | 0.0 | 6.85
|
||||
Comm | 0.0090909 | 0.0090909 | 0.0090909 | 0.0 | 0.39
|
||||
Output | 0.00069968 | 0.00069968 | 0.00069968 | 0.0 | 0.03
|
||||
Modify | 0.32099 | 0.32099 | 0.32099 | 0.0 | 13.75
|
||||
Other | | 0.002244 | | | 0.10
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 651 ave 651 max 651 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3388 ave 3388 max 3388 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3388
|
||||
Ave neighs/atom = 32.266667
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.4
Normal file
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.4
Normal file
@ -0,0 +1,141 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for Fe/O/H system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
Reading potential file ffield.reax.Fe_O_C_H with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.56 | 11.55 | 12.17 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||
100 127.3884 -9720.5854 0 -9681.0945 -933.74975
|
||||
200 141.21023 -9696.3143 0 -9652.5385 -831.74859
|
||||
300 176.81092 -9681.3376 0 -9626.5254 -520.29734
|
||||
400 220.75237 -9672.6195 0 -9604.1853 -388.89122
|
||||
500 301.29434 -9678.8461 0 -9585.4436 -545.24883
|
||||
600 320.36921 -9670.3055 0 -9570.9897 -609.45071
|
||||
700 414.5366 -9688.649 0 -9560.1409 -259.54271
|
||||
800 391.93079 -9675.1212 0 -9553.621 77.314405
|
||||
900 413.52641 -9673.738 0 -9545.5431 369.67477
|
||||
1000 382.02987 -9656.384 0 -9537.9531 236.57634
|
||||
1100 381.6811 -9647.4372 0 -9529.1144 -432.72725
|
||||
1200 470.68578 -9671.511 0 -9525.5964 448.88885
|
||||
1300 436.3616 -9659.2312 0 -9523.9573 188.07625
|
||||
1400 422.26867 -9651.2709 0 -9520.3658 48.829055
|
||||
1500 363.49419 -9625.6611 0 -9512.9764 -977.70396
|
||||
1600 450.39497 -9646.4762 0 -9506.8518 45.000339
|
||||
1700 461.44368 -9648.121 0 -9505.0715 -29.332359
|
||||
1800 457.02327 -9644.687 0 -9503.0078 -29.48478
|
||||
1900 461.60004 -9642.8571 0 -9499.7592 -608.0786
|
||||
2000 491.19069 -9648.6599 0 -9496.3887 -99.479995
|
||||
2100 461.50901 -9636.4581 0 -9493.3884 752.86874
|
||||
2200 480.7646 -9640.2431 0 -9491.204 -175.99562
|
||||
2300 450.00669 -9627.875 0 -9488.3711 -209.83065
|
||||
2400 475.84946 -9634.1191 0 -9486.6038 -366.65233
|
||||
2500 477.75601 -9631.4196 0 -9483.3132 558.18557
|
||||
2600 500.64305 -9636.9676 0 -9481.7661 111.76394
|
||||
2700 455.78826 -9620.2513 0 -9478.955 -962.65771
|
||||
2800 438.72349 -9611.8395 0 -9475.8334 -180.94976
|
||||
2900 471.33135 -9618.8641 0 -9472.7494 -291.14764
|
||||
3000 528.64651 -9636.4232 0 -9472.5405 111.18605
|
||||
Loop time of 1.42723 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 45.403 ns/day, 0.529 hours/ns, 2101.973 timesteps/s, 220.707 katom-step/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.79715 | 0.88663 | 0.96735 | 7.5 | 62.12
|
||||
Neigh | 0.083068 | 0.096787 | 0.10679 | 2.8 | 6.78
|
||||
Comm | 0.058539 | 0.13831 | 0.22776 | 19.0 | 9.69
|
||||
Output | 0.0006518 | 0.00071197 | 0.00088964 | 0.0 | 0.05
|
||||
Modify | 0.29308 | 0.30291 | 0.31706 | 1.6 | 21.22
|
||||
Other | | 0.001886 | | | 0.13
|
||||
|
||||
Nlocal: 26.25 ave 34 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 408 ave 462 max 347 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1109 ave 1419 max 453 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 4436
|
||||
Ave neighs/atom = 42.247619
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
@ -1,70 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# REAX potential for Fe/O/H system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
Reading potential file ffield.reax.Fe_O_C_H with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6 -> bins = 5 5 5
|
||||
Memory usage per processor = 17.7294 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||
3000 529.72301 -9636.7144 0 -9472.498 127.52152
|
||||
Loop time of 8.40814 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 7.707 ns/day, 3.114 hours/ns, 356.797 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.3193 | 7.3193 | 7.3193 | 0.0 | 87.05
|
||||
Neigh | 0.29032 | 0.29032 | 0.29032 | 0.0 | 3.45
|
||||
Comm | 0.016032 | 0.016032 | 0.016032 | 0.0 | 0.19
|
||||
Output | 1.2159e-05 | 1.2159e-05 | 1.2159e-05 | 0.0 | 0.00
|
||||
Modify | 0.77846 | 0.77846 | 0.77846 | 0.0 | 9.26
|
||||
Other | | 0.004053 | | | 0.05
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 651 ave 651 max 651 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3389 ave 3389 max 3389 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3389
|
||||
Ave neighs/atom = 32.2762
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:08
|
||||
@ -1,70 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
# REAX potential for Fe/O/H system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
Reading potential file ffield.reax.Fe_O_C_H with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6 -> bins = 5 5 5
|
||||
Memory usage per processor = 12.3695 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||
3000 534.48882 -9638.0405 0 -9472.3467 127.47989
|
||||
Loop time of 4.78344 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 13.547 ns/day, 1.772 hours/ns, 627.164 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.7061 | 3.7503 | 3.7853 | 1.5 | 78.40
|
||||
Neigh | 0.14361 | 0.16388 | 0.18297 | 3.4 | 3.43
|
||||
Comm | 0.062001 | 0.098492 | 0.14111 | 9.0 | 2.06
|
||||
Output | 2.0981e-05 | 2.2948e-05 | 2.7895e-05 | 0.1 | 0.00
|
||||
Modify | 0.75012 | 0.76764 | 0.78678 | 1.5 | 16.05
|
||||
Other | | 0.003105 | | | 0.06
|
||||
|
||||
Nlocal: 26.25 ave 35 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Nghost: 408 ave 462 max 348 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1107 ave 1428 max 453 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 4428
|
||||
Ave neighs/atom = 42.1714
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:05
|
||||
@ -12,16 +12,15 @@ atom_style charge
|
||||
atom_modify sort 100 0.0 # optional
|
||||
dimension 3
|
||||
boundary p p p
|
||||
box tilt large
|
||||
|
||||
read_data data.hns-equil
|
||||
replicate $x $y $z bbox
|
||||
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax.hns C H O N
|
||||
|
||||
compute reax all pair reax/c
|
||||
compute reax all pair reaxff
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
@ -35,6 +34,6 @@ thermo 10
|
||||
velocity all create 300.0 41279 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||
|
||||
run $t
|
||||
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.1
Normal file
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.1
Normal file
@ -0,0 +1,149 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
||||
# See README for more info
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
variable t index 100
|
||||
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
atom_modify sort 100 0.0 # optional
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.hns-equil
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (22.326 11.1412 13.778966) with tilt (0 -5.02603 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
304 atoms
|
||||
reading velocities ...
|
||||
304 velocities
|
||||
read_data CPU = 0.005 seconds
|
||||
replicate $x $y $z bbox
|
||||
replicate 2 $y $z bbox
|
||||
replicate 2 2 $z bbox
|
||||
replicate 2 2 2 bbox
|
||||
Replication is creating a 2x2x2 = 8 times larger system...
|
||||
triclinic box = (0 0 0) to (44.652 22.2824 27.557932) with tilt (0 -10.05206 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
bounding box image = (0 -1 -1) to (0 1 1)
|
||||
bounding box extra memory = 0.03 MB
|
||||
average # of replicas added to proc = 8.00 out of 8 (100.00%)
|
||||
2432 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax.hns C H O N
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
timestep 0.1
|
||||
|
||||
thermo_style custom step temp pe press evdwl ecoul vol
|
||||
thermo_modify norm yes
|
||||
thermo 10
|
||||
|
||||
velocity all create 300.0 41279 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||
|
||||
run $t
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 5 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 215 | 215 | 215 Mbytes
|
||||
Step Temp PotEng Press E_vdwl E_coul Volume
|
||||
0 300 -113.27833 437.52149 -111.57687 -1.7014647 27418.867
|
||||
10 299.38517 -113.27631 1439.2564 -111.57492 -1.7013814 27418.867
|
||||
20 300.27107 -113.27884 3764.4017 -111.57762 -1.7012246 27418.867
|
||||
30 302.21064 -113.28428 7007.6558 -111.58335 -1.7009364 27418.867
|
||||
40 303.52265 -113.28799 9844.8196 -111.58747 -1.7005186 27418.867
|
||||
50 301.8706 -113.28324 9663.08 -111.58318 -1.7000523 27418.867
|
||||
60 296.67808 -113.26777 7273.8875 -111.56815 -1.6996136 27418.867
|
||||
70 292.19999 -113.25435 5533.625 -111.55514 -1.6992157 27418.867
|
||||
80 293.58678 -113.25831 5993.4679 -111.55946 -1.6988532 27418.867
|
||||
90 300.62637 -113.27925 7202.8453 -111.58069 -1.6985592 27418.867
|
||||
100 305.38277 -113.29357 10085.747 -111.59518 -1.6983875 27418.867
|
||||
Loop time of 17.6114 on 1 procs for 100 steps with 2432 atoms
|
||||
|
||||
Performance: 0.049 ns/day, 489.205 hours/ns, 5.678 timesteps/s, 13.809 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.081 | 13.081 | 13.081 | 0.0 | 74.27
|
||||
Neigh | 0.25469 | 0.25469 | 0.25469 | 0.0 | 1.45
|
||||
Comm | 0.0061082 | 0.0061082 | 0.0061082 | 0.0 | 0.03
|
||||
Output | 0.00035315 | 0.00035315 | 0.00035315 | 0.0 | 0.00
|
||||
Modify | 4.2687 | 4.2687 | 4.2687 | 0.0 | 24.24
|
||||
Other | | 0.0007784 | | | 0.00
|
||||
|
||||
Nlocal: 2432 ave 2432 max 2432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10685 ave 10685 max 10685 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 823958 ave 823958 max 823958 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 823958
|
||||
Ave neighs/atom = 338.79852
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:17
|
||||
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.4
Normal file
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.4
Normal file
@ -0,0 +1,149 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
||||
# See README for more info
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
variable t index 100
|
||||
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
atom_modify sort 100 0.0 # optional
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.hns-equil
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (22.326 11.1412 13.778966) with tilt (0 -5.02603 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
304 atoms
|
||||
reading velocities ...
|
||||
304 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
replicate $x $y $z bbox
|
||||
replicate 2 $y $z bbox
|
||||
replicate 2 2 $z bbox
|
||||
replicate 2 2 2 bbox
|
||||
Replication is creating a 2x2x2 = 8 times larger system...
|
||||
triclinic box = (0 0 0) to (44.652 22.2824 27.557932) with tilt (0 -10.05206 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
bounding box image = (0 -1 -1) to (0 1 1)
|
||||
bounding box extra memory = 0.03 MB
|
||||
average # of replicas added to proc = 5.00 out of 8 (62.50%)
|
||||
2432 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
|
||||
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax.hns C H O N
|
||||
|
||||
compute reax all pair reaxff
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
timestep 0.1
|
||||
|
||||
thermo_style custom step temp pe press evdwl ecoul vol
|
||||
thermo_modify norm yes
|
||||
thermo 10
|
||||
|
||||
velocity all create 300.0 41279 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||
|
||||
run $t
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 5 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 103.8 | 103.8 | 103.8 Mbytes
|
||||
Step Temp PotEng Press E_vdwl E_coul Volume
|
||||
0 300 -113.27833 437.52125 -111.57687 -1.7014647 27418.867
|
||||
10 299.38517 -113.27631 1439.2564 -111.57492 -1.7013814 27418.867
|
||||
20 300.27106 -113.27884 3764.3691 -111.57762 -1.7012246 27418.867
|
||||
30 302.21062 -113.28428 7007.6981 -111.58335 -1.7009363 27418.867
|
||||
40 303.52264 -113.28799 9844.8446 -111.58747 -1.7005186 27418.867
|
||||
50 301.87059 -113.28324 9663.0539 -111.58318 -1.7000523 27418.867
|
||||
60 296.67807 -113.26777 7273.8306 -111.56815 -1.6996136 27418.867
|
||||
70 292.19997 -113.25435 5533.612 -111.55514 -1.6992157 27418.867
|
||||
80 293.58675 -113.25831 5993.4344 -111.55946 -1.6988533 27418.867
|
||||
90 300.62636 -113.27925 7202.8636 -111.58069 -1.6985591 27418.867
|
||||
100 305.38278 -113.29357 10085.719 -111.59518 -1.6983876 27418.867
|
||||
Loop time of 6.63333 on 4 procs for 100 steps with 2432 atoms
|
||||
|
||||
Performance: 0.130 ns/day, 184.259 hours/ns, 15.075 timesteps/s, 36.663 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.1006 | 4.5745 | 5.0624 | 17.4 | 68.96
|
||||
Neigh | 0.11589 | 0.11637 | 0.11669 | 0.1 | 1.75
|
||||
Comm | 0.0077297 | 0.49567 | 0.96958 | 52.7 | 7.47
|
||||
Output | 0.00027396 | 0.00031049 | 0.00038633 | 0.0 | 0.00
|
||||
Modify | 1.4458 | 1.4461 | 1.4465 | 0.0 | 21.80
|
||||
Other | | 0.0004201 | | | 0.01
|
||||
|
||||
Nlocal: 608 ave 612 max 604 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 5737.25 ave 5744 max 5732 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Neighs: 231539 ave 233090 max 229970 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 926155
|
||||
Ave neighs/atom = 380.82031
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:06
|
||||
@ -1,115 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
||||
# See README for more info
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
variable t index 100
|
||||
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
atom_modify sort 100 0.0 # optional
|
||||
dimension 3
|
||||
boundary p p p
|
||||
box tilt large
|
||||
|
||||
read_data data.hns-equil
|
||||
triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
304 atoms
|
||||
reading velocities ...
|
||||
304 velocities
|
||||
replicate $x $y $z bbox
|
||||
replicate 2 $y $z bbox
|
||||
replicate 2 2 $z bbox
|
||||
replicate 2 2 2 bbox
|
||||
triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2432 atoms
|
||||
Time spent = 0.000789404 secs
|
||||
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax.hns C H O N
|
||||
|
||||
compute reax all pair reax/c
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
timestep 0.1
|
||||
|
||||
thermo_style custom step temp pe press evdwl ecoul vol
|
||||
thermo_modify norm yes
|
||||
thermo 10
|
||||
|
||||
velocity all create 300.0 41279 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 5 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 262.4 | 262.4 | 262.4 Mbytes
|
||||
Step Temp PotEng Press E_vdwl E_coul Volume
|
||||
0 300 -113.27833 437.52103 -111.57687 -1.7014647 27418.867
|
||||
10 299.87174 -113.27778 2033.6337 -111.57645 -1.7013325 27418.867
|
||||
20 300.81718 -113.28046 4817.5889 -111.57931 -1.7011463 27418.867
|
||||
30 301.8622 -113.28323 8303.0039 -111.58237 -1.7008608 27418.867
|
||||
40 302.4646 -113.28493 10519.459 -111.58446 -1.700467 27418.867
|
||||
50 300.79064 -113.27989 10402.291 -111.57987 -1.7000218 27418.867
|
||||
60 296.11534 -113.26599 7929.1348 -111.5664 -1.6995929 27418.867
|
||||
70 291.73354 -113.25289 5071.5459 -111.5537 -1.6991916 27418.867
|
||||
80 292.189 -113.25399 5667.0962 -111.55519 -1.6987993 27418.867
|
||||
90 298.40792 -113.27253 7513.3806 -111.57409 -1.6984403 27418.867
|
||||
100 303.58246 -113.28809 10017.879 -111.58991 -1.698177 27418.867
|
||||
Loop time of 59.5461 on 1 procs for 100 steps with 2432 atoms
|
||||
|
||||
Performance: 0.015 ns/day, 1654.060 hours/ns, 1.679 timesteps/s
|
||||
97.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 49.922 | 49.922 | 49.922 | 0.0 | 83.84
|
||||
Neigh | 0.53154 | 0.53154 | 0.53154 | 0.0 | 0.89
|
||||
Comm | 0.011399 | 0.011399 | 0.011399 | 0.0 | 0.02
|
||||
Output | 0.00064397 | 0.00064397 | 0.00064397 | 0.0 | 0.00
|
||||
Modify | 9.0782 | 9.0782 | 9.0782 | 0.0 | 15.25
|
||||
Other | | 0.002116 | | | 0.00
|
||||
|
||||
Nlocal: 2432 ave 2432 max 2432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10687 ave 10687 max 10687 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 823977 ave 823977 max 823977 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 823977
|
||||
Ave neighs/atom = 338.806
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:00
|
||||
@ -1,115 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
||||
# See README for more info
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
variable t index 100
|
||||
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
atom_modify sort 100 0.0 # optional
|
||||
dimension 3
|
||||
boundary p p p
|
||||
box tilt large
|
||||
|
||||
read_data data.hns-equil
|
||||
triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
304 atoms
|
||||
reading velocities ...
|
||||
304 velocities
|
||||
replicate $x $y $z bbox
|
||||
replicate 2 $y $z bbox
|
||||
replicate 2 2 $z bbox
|
||||
replicate 2 2 2 bbox
|
||||
triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
2432 atoms
|
||||
Time spent = 0.000398397 secs
|
||||
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax.hns C H O N
|
||||
|
||||
compute reax all pair reax/c
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
timestep 0.1
|
||||
|
||||
thermo_style custom step temp pe press evdwl ecoul vol
|
||||
thermo_modify norm yes
|
||||
thermo 10
|
||||
|
||||
velocity all create 300.0 41279 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11
|
||||
ghost atom cutoff = 11
|
||||
binsize = 5.5, bins = 10 5 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 126.6 | 126.6 | 126.6 Mbytes
|
||||
Step Temp PotEng Press E_vdwl E_coul Volume
|
||||
0 300 -113.27833 437.52112 -111.57687 -1.7014647 27418.867
|
||||
10 299.87174 -113.27778 2033.632 -111.57645 -1.7013325 27418.867
|
||||
20 300.81719 -113.28046 4817.5761 -111.57931 -1.7011463 27418.867
|
||||
30 301.8622 -113.28323 8302.9767 -111.58237 -1.7008609 27418.867
|
||||
40 302.4646 -113.28493 10519.481 -111.58446 -1.700467 27418.867
|
||||
50 300.79064 -113.27989 10402.312 -111.57987 -1.7000217 27418.867
|
||||
60 296.11534 -113.26599 7929.1393 -111.5664 -1.6995929 27418.867
|
||||
70 291.73354 -113.25289 5071.5368 -111.5537 -1.6991916 27418.867
|
||||
80 292.18901 -113.25399 5667.1118 -111.55519 -1.6987993 27418.867
|
||||
90 298.40793 -113.27253 7513.4029 -111.57409 -1.6984403 27418.867
|
||||
100 303.58247 -113.28809 10017.892 -111.58991 -1.698177 27418.867
|
||||
Loop time of 21.3933 on 4 procs for 100 steps with 2432 atoms
|
||||
|
||||
Performance: 0.040 ns/day, 594.257 hours/ns, 4.674 timesteps/s
|
||||
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.863 | 16.367 | 18.027 | 28.6 | 76.51
|
||||
Neigh | 0.23943 | 0.2422 | 0.24658 | 0.6 | 1.13
|
||||
Comm | 0.024331 | 1.6845 | 3.189 | 89.2 | 7.87
|
||||
Output | 0.00051165 | 0.00056899 | 0.00068665 | 0.0 | 0.00
|
||||
Modify | 3.0933 | 3.0969 | 3.0999 | 0.1 | 14.48
|
||||
Other | | 0.001784 | | | 0.01
|
||||
|
||||
Nlocal: 608 ave 608 max 608 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5738.25 ave 5742 max 5734 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 231544 ave 231625 max 231466 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 926176
|
||||
Ave neighs/atom = 380.829
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:21
|
||||
@ -1,23 +1,23 @@
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
run 3000
|
||||
|
||||
@ -1,17 +1,8 @@
|
||||
simulation_name RDX_example ! output files will carry this name + their specific ext
|
||||
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
energy_update_freq 1
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
write_freq 1 ! write trajectory after so many steps
|
||||
traj_title RDX ! (no white spaces)
|
||||
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
|
||||
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
|
||||
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
|
||||
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
|
||||
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
|
||||
|
||||
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.1
Normal file
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.1
Normal file
@ -0,0 +1,140 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.3 | 16.3 | 16.3 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
100 47.478574 -10176.425 0 -10161.706 632.99863
|
||||
200 166.95277 -10181.513 0 -10129.757 -27.107717
|
||||
300 142.53594 -10148.039 0 -10103.853 5120.6794
|
||||
400 322.68495 -10178.868 0 -10078.834 2342.89
|
||||
500 193.81476 -10117.984 0 -10057.901 8412.5289
|
||||
600 300.27155 -10134.473 0 -10041.388 -2801.8661
|
||||
700 272.63426 -10110.146 0 -10025.629 10749.023
|
||||
800 339.99867 -10114.124 0 -10008.723 5122.9966
|
||||
900 231.65547 -10068.587 0 -9996.7728 5306.059
|
||||
1000 329.92918 -10088.776 0 -9986.4964 3190.1697
|
||||
1100 376.60905 -10092.398 0 -9975.6476 2921.9605
|
||||
1200 361.98746 -10076.599 0 -9964.3813 3612.0455
|
||||
1300 358.65631 -10069.365 0 -9958.1802 4339.8435
|
||||
1400 470.15262 -10098.553 0 -9952.8035 -146.0811
|
||||
1500 509.62274 -10106.57 0 -9948.5844 2356.8592
|
||||
1600 417.89364 -10075.274 0 -9945.7249 1760.5655
|
||||
1700 453.21317 -10084.329 0 -9943.8306 -570.32375
|
||||
1800 472.92112 -10087.83 0 -9941.2221 1550.3495
|
||||
1900 507.18794 -10096.441 0 -9939.2102 -460.65809
|
||||
2000 443.55347 -10076.832 0 -9939.3281 -145.14295
|
||||
2100 485.44451 -10088.451 0 -9937.9611 -614.40787
|
||||
2200 507.52411 -10095.157 0 -9937.8226 1308.3869
|
||||
2300 496.44961 -10089.637 0 -9935.7354 206.44147
|
||||
2400 457.99343 -10078.114 0 -9936.1344 810.80538
|
||||
2500 507.88115 -10092.692 0 -9935.2463 -464.87873
|
||||
2600 437.84198 -10069.789 0 -9934.0561 1323.4191
|
||||
2700 503.09017 -10088.945 0 -9932.9853 1133.3561
|
||||
2800 481.73908 -10082.193 0 -9932.852 -27.838881
|
||||
2900 487.56555 -10082.752 0 -9931.6045 1772.2131
|
||||
3000 510.30601 -10091.368 0 -9933.1706 1273.0501
|
||||
Loop time of 5.35022 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 12.112 ns/day, 1.982 hours/ns, 560.725 timesteps/s, 58.876 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.7927 | 4.7927 | 4.7927 | 0.0 | 89.58
|
||||
Neigh | 0.15169 | 0.15169 | 0.15169 | 0.0 | 2.84
|
||||
Comm | 0.011036 | 0.011036 | 0.011036 | 0.0 | 0.21
|
||||
Output | 0.00080628 | 0.00080628 | 0.00080628 | 0.0 | 0.02
|
||||
Modify | 0.3906 | 0.3906 | 0.3906 | 0.0 | 7.30
|
||||
Other | | 0.003436 | | | 0.06
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 645 ave 645 max 645 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3065 ave 3065 max 3065 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3065
|
||||
Ave neighs/atom = 29.190476
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:05
|
||||
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.4
Normal file
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.4
Normal file
@ -0,0 +1,140 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.78 | 11.56 | 12.26 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
100 47.47852 -10176.425 0 -10161.706 632.97359
|
||||
200 166.95287 -10181.513 0 -10129.757 -27.146803
|
||||
300 142.53582 -10148.039 0 -10103.852 5120.6397
|
||||
400 322.68523 -10178.868 0 -10078.834 2342.7187
|
||||
500 193.81484 -10117.984 0 -10057.901 8412.4559
|
||||
600 300.27165 -10134.473 0 -10041.388 -2801.9143
|
||||
700 272.63408 -10110.146 0 -10025.629 10749.2
|
||||
800 339.99669 -10114.123 0 -10008.723 5123.2489
|
||||
900 231.65632 -10068.587 0 -9996.7729 5306.0392
|
||||
1000 329.93324 -10088.777 0 -9986.4967 3190.4707
|
||||
1100 376.60924 -10092.398 0 -9975.6478 2920.8475
|
||||
1200 361.98231 -10076.598 0 -9964.3816 3612.0573
|
||||
1300 358.6599 -10069.366 0 -9958.1803 4341.9871
|
||||
1400 470.14856 -10098.552 0 -9952.8036 -146.9069
|
||||
1500 509.6454 -10106.577 0 -9948.5847 2355.4022
|
||||
1600 417.9276 -10075.284 0 -9945.7249 1749.565
|
||||
1700 453.25817 -10084.343 0 -9943.8306 -570.48011
|
||||
1800 472.9517 -10087.84 0 -9941.2226 1532.6424
|
||||
1900 507.14171 -10096.428 0 -9939.212 -404.84948
|
||||
2000 443.62843 -10076.86 0 -9939.3329 -132.17302
|
||||
2100 485.441 -10088.414 0 -9937.925 -609.75758
|
||||
2200 507.23914 -10095.067 0 -9937.8209 1288.5372
|
||||
2300 499.64956 -10090.665 0 -9935.7719 149.06622
|
||||
2400 457.97848 -10078.107 0 -9936.1317 2065.2075
|
||||
2500 510.58254 -10093.537 0 -9935.2543 -559.75965
|
||||
2600 440.97503 -10070.865 0 -9934.1605 1164.1078
|
||||
2700 500.4945 -10088.165 0 -9933.0096 1051.9016
|
||||
2800 485.77814 -10083.543 0 -9932.9498 294.64404
|
||||
2900 487.73983 -10082.939 0 -9931.7373 2208.263
|
||||
3000 504.69717 -10089.803 0 -9933.3447 1723.6386
|
||||
Loop time of 2.81192 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 23.045 ns/day, 1.041 hours/ns, 1066.887 timesteps/s, 112.023 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0513 | 2.1567 | 2.2232 | 4.3 | 76.70
|
||||
Neigh | 0.072125 | 0.087048 | 0.10214 | 3.7 | 3.10
|
||||
Comm | 0.086792 | 0.15326 | 0.25749 | 16.2 | 5.45
|
||||
Output | 0.00058533 | 0.00064027 | 0.00080207 | 0.0 | 0.02
|
||||
Modify | 0.39587 | 0.41124 | 0.42647 | 1.7 | 14.62
|
||||
Other | | 0.003062 | | | 0.11
|
||||
|
||||
Nlocal: 26.25 ave 46 max 8 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 399.5 ave 512 max 288 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1011.25 ave 1819 max 420 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4045
|
||||
Ave neighs/atom = 38.52381
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:02
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 19 | 19 | 19 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
3000 510.63767 -10091.537 0 -9933.2374 1144.545
|
||||
Loop time of 21.2931 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 3.043 ns/day, 7.886 hours/ns, 140.891 timesteps/s
|
||||
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.887 | 19.887 | 19.887 | 0.0 | 93.40
|
||||
Neigh | 0.33143 | 0.33143 | 0.33143 | 0.0 | 1.56
|
||||
Comm | 0.02079 | 0.02079 | 0.02079 | 0.0 | 0.10
|
||||
Output | 2.5272e-05 | 2.5272e-05 | 2.5272e-05 | 0.0 | 0.00
|
||||
Modify | 1.0478 | 1.0478 | 1.0478 | 0.0 | 4.92
|
||||
Other | | 0.006125 | | | 0.03
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 645 ave 645 max 645 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3063 ave 3063 max 3063 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3063
|
||||
Ave neighs/atom = 29.1714
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:21
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.14 | 13.04 | 13.9 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
3000 509.89257 -10091.36 0 -9933.2916 1406.1215
|
||||
Loop time of 10.8858 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 5.953 ns/day, 4.032 hours/ns, 275.588 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.3081 | 9.4054 | 9.4994 | 2.6 | 86.40
|
||||
Neigh | 0.15541 | 0.18258 | 0.2099 | 4.7 | 1.68
|
||||
Comm | 0.070516 | 0.16621 | 0.26541 | 19.7 | 1.53
|
||||
Output | 2.2173e-05 | 2.5153e-05 | 3.3855e-05 | 0.0 | 0.00
|
||||
Modify | 1.0979 | 1.1272 | 1.1568 | 2.1 | 10.35
|
||||
Other | | 0.004379 | | | 0.04
|
||||
|
||||
Nlocal: 26.25 ave 46 max 8 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 399.5 ave 512 max 288 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1011.25 ave 1819 max 420 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4045
|
||||
Ave neighs/atom = 38.5238
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:11
|
||||
@ -1,23 +1,23 @@
|
||||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
|
||||
run 3000
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
thermo 100
|
||||
run 2000
|
||||
|
||||
@ -1,17 +1,8 @@
|
||||
simulation_name VOH_example ! output files will carry this name + their specific ext
|
||||
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
energy_update_freq 1
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
write_freq 1 ! write trajectory after so many steps
|
||||
traj_title VOH ! (no white spaces)
|
||||
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
|
||||
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
|
||||
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
|
||||
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
|
||||
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
|
||||
|
||||
131
examples/reaxff/VOH/log.30Nov23.VOH.g++.1
Normal file
131
examples/reaxff/VOH/log.30Nov23.VOH.g++.1
Normal file
@ -0,0 +1,131 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
thermo 100
|
||||
run 2000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.34 | 15.34 | 15.34 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10246.825 0 -10246.825 42.256089
|
||||
100 83.813625 -10238.056 0 -10213.322 -246.37234
|
||||
200 128.47312 -10221.424 0 -10183.511 -896.05588
|
||||
300 199.45833 -10218.343 0 -10159.482 -66.676466
|
||||
400 243.93496 -10211.648 0 -10139.663 -1073.274
|
||||
500 314.81116 -10216.592 0 -10123.692 542.54772
|
||||
600 361.45977 -10217.717 0 -10111.05 205.47425
|
||||
700 392.16954 -10215.815 0 -10100.086 -283.06967
|
||||
800 392.49036 -10206.909 0 -10091.085 953.23712
|
||||
900 426.51015 -10209.352 0 -10083.489 473.9928
|
||||
1000 398.23517 -10195.103 0 -10077.584 243.59494
|
||||
1100 414.05403 -10192.081 0 -10069.893 1063.7609
|
||||
1200 442.70037 -10196.631 0 -10065.99 -1189.773
|
||||
1300 470.32545 -10201.252 0 -10062.459 -132.3016
|
||||
1400 446.97236 -10189.078 0 -10057.176 9.8938187
|
||||
1500 475.7665 -10195.598 0 -10055.199 -877.81691
|
||||
1600 440.45154 -10181.071 0 -10051.093 579.85471
|
||||
1700 517.45211 -10201.067 0 -10048.367 136.58133
|
||||
1800 461.86671 -10182.818 0 -10046.521 -260.09694
|
||||
1900 463.99242 -10181.136 0 -10044.211 1567.8398
|
||||
2000 476.73786 -10184.032 0 -10043.346 -883.50859
|
||||
Loop time of 1.94324 on 1 procs for 2000 steps with 100 atoms
|
||||
|
||||
Performance: 22.231 ns/day, 1.080 hours/ns, 1029.207 timesteps/s, 102.921 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5707 | 1.5707 | 1.5707 | 0.0 | 80.83
|
||||
Neigh | 0.1054 | 0.1054 | 0.1054 | 0.0 | 5.42
|
||||
Comm | 0.005606 | 0.005606 | 0.005606 | 0.0 | 0.29
|
||||
Output | 0.00053398 | 0.00053398 | 0.00053398 | 0.0 | 0.03
|
||||
Modify | 0.2594 | 0.2594 | 0.2594 | 0.0 | 13.35
|
||||
Other | | 0.001603 | | | 0.08
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 638 ave 638 max 638 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3434 ave 3434 max 3434 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3434
|
||||
Ave neighs/atom = 34.34
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
131
examples/reaxff/VOH/log.30Nov23.VOH.g++.4
Normal file
131
examples/reaxff/VOH/log.30Nov23.VOH.g++.4
Normal file
@ -0,0 +1,131 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
thermo 100
|
||||
run 2000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.04 | 11.12 | 12.06 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10246.825 0 -10246.825 42.256092
|
||||
100 83.813732 -10238.056 0 -10213.322 -246.39794
|
||||
200 128.4729 -10221.424 0 -10183.511 -896.07308
|
||||
300 199.45765 -10218.342 0 -10159.482 -66.695871
|
||||
400 243.93632 -10211.649 0 -10139.663 -1073.2779
|
||||
500 314.81228 -10216.592 0 -10123.691 542.5312
|
||||
600 361.46099 -10217.717 0 -10111.05 205.56032
|
||||
700 392.16903 -10215.815 0 -10100.086 -283.00265
|
||||
800 392.48962 -10206.909 0 -10091.085 953.23878
|
||||
900 426.50866 -10209.352 0 -10083.489 474.04312
|
||||
1000 398.23724 -10195.104 0 -10077.584 243.52194
|
||||
1100 414.05514 -10192.081 0 -10069.893 1063.726
|
||||
1200 442.70432 -10196.633 0 -10065.99 -1189.8309
|
||||
1300 470.32067 -10201.251 0 -10062.459 -132.41831
|
||||
1400 447.00366 -10189.087 0 -10057.177 10.168781
|
||||
1500 475.77239 -10195.599 0 -10055.199 -877.85409
|
||||
1600 440.43788 -10181.066 0 -10051.092 580.25473
|
||||
1700 517.37824 -10201.044 0 -10048.366 136.09841
|
||||
1800 461.75464 -10182.78 0 -10046.517 -259.88878
|
||||
1900 464.0812 -10181.158 0 -10044.207 1566.4734
|
||||
2000 476.55134 -10183.975 0 -10043.344 -884.37537
|
||||
Loop time of 1.16101 on 4 procs for 2000 steps with 100 atoms
|
||||
|
||||
Performance: 37.209 ns/day, 0.645 hours/ns, 1722.640 timesteps/s, 172.264 katom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.65447 | 0.69002 | 0.77443 | 6.0 | 59.43
|
||||
Neigh | 0.050397 | 0.060259 | 0.06883 | 2.7 | 5.19
|
||||
Comm | 0.03061 | 0.1145 | 0.15016 | 14.5 | 9.86
|
||||
Output | 0.00039488 | 0.00043537 | 0.00055434 | 0.0 | 0.04
|
||||
Modify | 0.28585 | 0.29446 | 0.30467 | 1.2 | 25.36
|
||||
Other | | 0.00134 | | | 0.12
|
||||
|
||||
Nlocal: 25 ave 36 max 10 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Nghost: 385.75 ave 472 max 299 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1077 ave 1693 max 379 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 4308
|
||||
Ave neighs/atom = 43.08
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:01
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.79 | 17.79 | 17.79 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10246.825 0 -10246.825 42.256089
|
||||
3000 476.73301 -10185.256 0 -10044.572 -694.70737
|
||||
Loop time of 11.0577 on 1 procs for 3000 steps with 100 atoms
|
||||
|
||||
Performance: 5.860 ns/day, 4.095 hours/ns, 271.304 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.6785 | 9.6785 | 9.6785 | 0.0 | 87.53
|
||||
Neigh | 0.32599 | 0.32599 | 0.32599 | 0.0 | 2.95
|
||||
Comm | 0.017231 | 0.017231 | 0.017231 | 0.0 | 0.16
|
||||
Output | 2.5511e-05 | 2.5511e-05 | 2.5511e-05 | 0.0 | 0.00
|
||||
Modify | 1.0311 | 1.0311 | 1.0311 | 0.0 | 9.32
|
||||
Other | | 0.004857 | | | 0.04
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 598 ave 598 max 598 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3390 ave 3390 max 3390 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3390
|
||||
Ave neighs/atom = 33.9
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:11
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.21 | 12.52 | 13.64 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10246.825 0 -10246.825 42.256092
|
||||
3000 489.67803 -10188.866 0 -10044.362 -553.7513
|
||||
Loop time of 6.49847 on 4 procs for 3000 steps with 100 atoms
|
||||
|
||||
Performance: 9.972 ns/day, 2.407 hours/ns, 461.647 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.7412 | 4.8453 | 4.9104 | 2.9 | 74.56
|
||||
Neigh | 0.1468 | 0.17834 | 0.20151 | 4.7 | 2.74
|
||||
Comm | 0.071841 | 0.14037 | 0.24502 | 17.2 | 2.16
|
||||
Output | 2.1219e-05 | 2.408e-05 | 3.1948e-05 | 0.0 | 0.00
|
||||
Modify | 1.3072 | 1.3308 | 1.3627 | 1.7 | 20.48
|
||||
Other | | 0.003713 | | | 0.06
|
||||
|
||||
Nlocal: 25 ave 38 max 11 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 369.75 ave 453 max 283 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 1082.25 ave 1788 max 417 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 4329
|
||||
Ave neighs/atom = 43.29
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,23 +1,24 @@
|
||||
# REAX potential for ZnOH2 system
|
||||
# .....
|
||||
|
||||
units real
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
|
||||
run 3000
|
||||
run 1000
|
||||
|
||||
@ -1,17 +1,7 @@
|
||||
simulation_name ZnOH2_example ! output files will carry this name + their specific ext
|
||||
|
||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
||||
energy_update_freq 1
|
||||
|
||||
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||
|
||||
write_freq 1 ! write trajectory after so many steps
|
||||
traj_title ZnOH2 ! (no white spaces)
|
||||
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
|
||||
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
|
||||
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
|
||||
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
|
||||
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
|
||||
|
||||
122
examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.1
Normal file
122
examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.1
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for ZnOH2 system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
Reading potential file ffield.reax.ZnOH with DATE: 2011-02-18
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.8 | 15.8 | 15.8 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -7900.2668 0 -7900.2668 60.076093
|
||||
100 89.745108 -7892.7937 0 -7864.9724 -359.37879
|
||||
200 151.73431 -7883.2823 0 -7836.244 118.04838
|
||||
300 223.74392 -7881.6513 0 -7812.2898 -97.069674
|
||||
400 293.70909 -7883.7754 0 -7792.7243 -384.10332
|
||||
500 301.22843 -7869.313 0 -7775.9309 76.604433
|
||||
600 317.45476 -7860.4665 0 -7762.0541 40.95095
|
||||
700 335.70939 -7853.865 0 -7749.7937 -173.3119
|
||||
800 380.48725 -7857.8679 0 -7739.9152 -139.88773
|
||||
900 502.93129 -7891.7095 0 -7735.7987 488.40109
|
||||
1000 510.36735 -7894.0653 0 -7735.8493 -222.85193
|
||||
Loop time of 0.583996 on 1 procs for 1000 steps with 105 atoms
|
||||
|
||||
Performance: 36.987 ns/day, 0.649 hours/ns, 1712.342 timesteps/s, 179.796 katom-step/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41526 | 0.41526 | 0.41526 | 0.0 | 71.11
|
||||
Neigh | 0.058908 | 0.058908 | 0.058908 | 0.0 | 10.09
|
||||
Comm | 0.0028308 | 0.0028308 | 0.0028308 | 0.0 | 0.48
|
||||
Output | 0.00021295 | 0.00021295 | 0.00021295 | 0.0 | 0.04
|
||||
Modify | 0.1061 | 0.1061 | 0.1061 | 0.0 | 18.17
|
||||
Other | | 0.0006844 | | | 0.12
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 640 ave 640 max 640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3934 ave 3934 max 3934 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3934
|
||||
Ave neighs/atom = 37.466667
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
122
examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.4
Normal file
122
examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.4
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for ZnOH2 system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style reaxff lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
Reading potential file ffield.reax.ZnOH with DATE: 2011-02-18
|
||||
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.1 | 11.34 | 12.51 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -7900.2668 0 -7900.2668 60.076093
|
||||
100 89.745102 -7892.7938 0 -7864.9724 -359.39279
|
||||
200 151.73402 -7883.2823 0 -7836.2441 118.03582
|
||||
300 223.74416 -7881.6514 0 -7812.2897 -97.060088
|
||||
400 293.70926 -7883.7754 0 -7792.7242 -384.10477
|
||||
500 301.22851 -7869.3129 0 -7775.9308 76.601414
|
||||
600 317.45436 -7860.4664 0 -7762.0542 40.946828
|
||||
700 335.70975 -7853.8651 0 -7749.7936 -173.31084
|
||||
800 380.48744 -7857.868 0 -7739.9153 -139.87915
|
||||
900 502.93034 -7891.7094 0 -7735.7989 488.3973
|
||||
1000 510.36634 -7894.0651 0 -7735.8493 -222.85474
|
||||
Loop time of 0.345754 on 4 procs for 1000 steps with 105 atoms
|
||||
|
||||
Performance: 62.472 ns/day, 0.384 hours/ns, 2892.228 timesteps/s, 303.684 katom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.18043 | 0.18884 | 0.19544 | 1.3 | 54.62
|
||||
Neigh | 0.027479 | 0.033519 | 0.039456 | 2.3 | 9.69
|
||||
Comm | 0.01673 | 0.023479 | 0.031605 | 3.6 | 6.79
|
||||
Output | 0.00019732 | 0.0002106 | 0.00024979 | 0.0 | 0.06
|
||||
Modify | 0.093437 | 0.099224 | 0.10519 | 1.3 | 28.70
|
||||
Other | | 0.0004842 | | | 0.14
|
||||
|
||||
Nlocal: 26.25 ave 41 max 11 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 390.25 ave 491 max 286 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 1154 ave 1912 max 445 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4616
|
||||
Ave neighs/atom = 43.961905
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for ZnOH2 system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
Reading potential file ffield.reax.ZnOH with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.36 | 18.36 | 18.36 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -7900.2668 0 -7900.2668 60.076093
|
||||
3000 535.58577 -7934.7287 0 -7768.6948 -475.46237
|
||||
Loop time of 7.29784 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 8.879 ns/day, 2.703 hours/ns, 411.081 timesteps/s
|
||||
97.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.9988 | 5.9988 | 5.9988 | 0.0 | 82.20
|
||||
Neigh | 0.37455 | 0.37455 | 0.37455 | 0.0 | 5.13
|
||||
Comm | 0.019186 | 0.019186 | 0.019186 | 0.0 | 0.26
|
||||
Output | 2.4557e-05 | 2.4557e-05 | 2.4557e-05 | 0.0 | 0.00
|
||||
Modify | 0.89915 | 0.89915 | 0.89915 | 0.0 | 12.32
|
||||
Other | | 0.006108 | | | 0.08
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 649 ave 649 max 649 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3971 ave 3971 max 3971 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3971
|
||||
Ave neighs/atom = 37.819
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# REAX potential for ZnOH2 system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
Reading potential file ffield.reax.ZnOH with DATE: 2011-02-18
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
|
||||
run 3000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off, ghost
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.28 | 12.77 | 14.21 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -7900.2668 0 -7900.2668 60.076093
|
||||
3000 538.25796 -7935.6159 0 -7768.7536 -525.47078
|
||||
Loop time of 4.48824 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Performance: 14.438 ns/day, 1.662 hours/ns, 668.414 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.1031 | 3.1698 | 3.2378 | 3.3 | 70.62
|
||||
Neigh | 0.16642 | 0.20502 | 0.25003 | 6.6 | 4.57
|
||||
Comm | 0.074932 | 0.14224 | 0.21025 | 15.6 | 3.17
|
||||
Output | 0.00011349 | 0.00011736 | 0.00012231 | 0.0 | 0.00
|
||||
Modify | 0.92089 | 0.96736 | 1.0083 | 3.2 | 21.55
|
||||
Other | | 0.003731 | | | 0.08
|
||||
|
||||
Nlocal: 26.25 ave 45 max 15 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 399 ave 509 max 295 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Neighs: 1151.5 ave 2066 max 701 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4606
|
||||
Ave neighs/atom = 43.8667
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds not checked
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:04
|
||||
@ -4,8 +4,8 @@ units real
|
||||
|
||||
read_data CH4.dat
|
||||
|
||||
pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
|
||||
pair_coeff * * reax/c ffield.ci-reax.CH C H
|
||||
pair_style hybrid/overlay reaxff control checkqeq no table linear 11000
|
||||
pair_coeff * * reaxff ffield.ci-reax.CH C H
|
||||
pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
|
||||
pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
|
||||
pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
|
||||
|
||||
105
examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.1
Normal file
105
examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.1
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
#ci-reax potential for CH systems with tabulated ZBL correction
|
||||
atom_style charge
|
||||
units real
|
||||
|
||||
read_data CH4.dat
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
315 atoms
|
||||
reading velocities ...
|
||||
315 velocities
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
pair_style hybrid/overlay reaxff control checkqeq no table linear 11000
|
||||
pair_coeff * * reaxff ffield.ci-reax.CH C H
|
||||
Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
|
||||
pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
|
||||
WARNING: 2 of 10000 force values in table CC_cireaxFF are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
|
||||
WARNING: 2 of 11000 force values in table CH_cireaxFF are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
|
||||
WARNING: 2 of 6000 force values in table HH_cireaxFF are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
|
||||
timestep 0.25
|
||||
fix 1 all nve
|
||||
fix 2 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
#dump 1 all atom 30 dump.ci-reax.lammpstrj
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (src/REAXFF/pair_reaxff.cpp:365)
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 9.5
|
||||
ghost atom cutoff = 9.5
|
||||
binsize = 4.75, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair table, perpetual
|
||||
attributes: half, newton on, cut 3.1
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.64 | 35.64 | 35.64 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 508.42043 -28736.654 0 -28260.785 1678.3276
|
||||
3000 480.41333 -28707.835 0 -28258.181 -3150.0762
|
||||
Loop time of 13.2263 on 1 procs for 3000 steps with 315 atoms
|
||||
|
||||
Performance: 4.899 ns/day, 4.899 hours/ns, 226.821 timesteps/s, 71.449 katom-step/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.046 | 13.046 | 13.046 | 0.0 | 98.64
|
||||
Neigh | 0.12783 | 0.12783 | 0.12783 | 0.0 | 0.97
|
||||
Comm | 0.025611 | 0.025611 | 0.025611 | 0.0 | 0.19
|
||||
Output | 2.2361e-05 | 2.2361e-05 | 2.2361e-05 | 0.0 | 0.00
|
||||
Modify | 0.017722 | 0.017722 | 0.017722 | 0.0 | 0.13
|
||||
Other | | 0.008824 | | | 0.07
|
||||
|
||||
Nlocal: 315 ave 315 max 315 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2056 ave 2056 max 2056 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 32754 ave 32754 max 32754 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 32754
|
||||
Ave neighs/atom = 103.98095
|
||||
Neighbor list builds = 37
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:13
|
||||
105
examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.4
Normal file
105
examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.4
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
#ci-reax potential for CH systems with tabulated ZBL correction
|
||||
atom_style charge
|
||||
units real
|
||||
|
||||
read_data CH4.dat
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
315 atoms
|
||||
reading velocities ...
|
||||
315 velocities
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_style hybrid/overlay reaxff control checkqeq no table linear 11000
|
||||
pair_coeff * * reaxff ffield.ci-reax.CH C H
|
||||
Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
|
||||
pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
|
||||
WARNING: 2 of 10000 force values in table CC_cireaxFF are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
|
||||
WARNING: 2 of 11000 force values in table CH_cireaxFF are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
|
||||
WARNING: 2 of 6000 force values in table HH_cireaxFF are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
|
||||
timestep 0.25
|
||||
fix 1 all nve
|
||||
fix 2 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
#dump 1 all atom 30 dump.ci-reax.lammpstrj
|
||||
|
||||
run 3000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (src/REAXFF/pair_reaxff.cpp:365)
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 9.5
|
||||
ghost atom cutoff = 9.5
|
||||
binsize = 4.75, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair table, perpetual
|
||||
attributes: half, newton on, cut 3.1
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 20.4 | 21.35 | 22.73 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 508.42043 -28736.654 0 -28260.785 1678.3276
|
||||
3000 480.41333 -28707.835 0 -28258.181 -3150.0762
|
||||
Loop time of 8.18251 on 4 procs for 3000 steps with 315 atoms
|
||||
|
||||
Performance: 7.919 ns/day, 3.031 hours/ns, 366.636 timesteps/s, 115.490 katom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.7983 | 7.3808 | 7.9976 | 16.3 | 90.20
|
||||
Neigh | 0.062309 | 0.065996 | 0.07006 | 1.4 | 0.81
|
||||
Comm | 0.083586 | 0.70629 | 1.2934 | 53.1 | 8.63
|
||||
Output | 1.8365e-05 | 2.0853e-05 | 2.7615e-05 | 0.0 | 0.00
|
||||
Modify | 0.016829 | 0.019422 | 0.02157 | 1.4 | 0.24
|
||||
Other | | 0.01001 | | | 0.12
|
||||
|
||||
Nlocal: 78.75 ave 96 max 65 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1233 ave 1348 max 1116 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 9467.25 ave 12150 max 7160 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 37869
|
||||
Ave neighs/atom = 120.21905
|
||||
Neighbor list builds = 37
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
@ -1,86 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
#ci-reax potential for CH systems with tabulated ZBL correction
|
||||
atom_style charge
|
||||
units real
|
||||
|
||||
read_data CH4.dat
|
||||
orthogonal box = (0 0 0) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
315 atoms
|
||||
reading velocities ...
|
||||
315 velocities
|
||||
|
||||
pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
|
||||
pair_coeff * * reax/c ffield.ci-reax.CH C H
|
||||
Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
|
||||
pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
|
||||
WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
|
||||
WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
|
||||
WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
|
||||
timestep 0.25
|
||||
fix 1 all nve
|
||||
fix 2 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
#dump 1 all atom 30 dump.ci-reax.lammpstrj
|
||||
|
||||
run 3000
|
||||
WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 9.5
|
||||
ghost atom cutoff = 9.5
|
||||
binsize = 4.75, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 43.46 | 43.46 | 43.46 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 508.42043 -28736.654 0 -28260.785 1678.3276
|
||||
3000 480.41333 -28707.835 0 -28258.181 -3150.0762
|
||||
Loop time of 45.3959 on 1 procs for 3000 steps with 315 atoms
|
||||
|
||||
Performance: 1.427 ns/day, 16.813 hours/ns, 66.085 timesteps/s
|
||||
96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 44.955 | 44.955 | 44.955 | 0.0 | 99.03
|
||||
Neigh | 0.29903 | 0.29903 | 0.29903 | 0.0 | 0.66
|
||||
Comm | 0.056547 | 0.056547 | 0.056547 | 0.0 | 0.12
|
||||
Output | 4.8399e-05 | 4.8399e-05 | 4.8399e-05 | 0.0 | 0.00
|
||||
Modify | 0.058722 | 0.058722 | 0.058722 | 0.0 | 0.13
|
||||
Other | | 0.02632 | | | 0.06
|
||||
|
||||
Nlocal: 315 ave 315 max 315 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2056 ave 2056 max 2056 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 32754 ave 32754 max 32754 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 32754
|
||||
Ave neighs/atom = 103.981
|
||||
Neighbor list builds = 37
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:45
|
||||
@ -1,86 +0,0 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
#ci-reax potential for CH systems with tabulated ZBL correction
|
||||
atom_style charge
|
||||
units real
|
||||
|
||||
read_data CH4.dat
|
||||
orthogonal box = (0 0 0) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
315 atoms
|
||||
reading velocities ...
|
||||
315 velocities
|
||||
|
||||
pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
|
||||
pair_coeff * * reax/c ffield.ci-reax.CH C H
|
||||
Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
|
||||
pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
|
||||
WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
|
||||
WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
|
||||
WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
|
||||
timestep 0.25
|
||||
fix 1 all nve
|
||||
fix 2 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
#dump 1 all atom 30 dump.ci-reax.lammpstrj
|
||||
|
||||
run 3000
|
||||
WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 9.5
|
||||
ghost atom cutoff = 9.5
|
||||
binsize = 4.75, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reax/c, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: half/ghost/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 24.48 | 25.61 | 27.27 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 508.42043 -28736.654 0 -28260.785 1678.3276
|
||||
3000 480.41333 -28707.835 0 -28258.181 -3150.0762
|
||||
Loop time of 24.7034 on 4 procs for 3000 steps with 315 atoms
|
||||
|
||||
Performance: 2.623 ns/day, 9.149 hours/ns, 121.441 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.945 | 21.367 | 24.046 | 39.3 | 86.49
|
||||
Neigh | 0.1456 | 0.15254 | 0.16101 | 1.6 | 0.62
|
||||
Comm | 0.39168 | 3.0859 | 5.5185 | 103.9 | 12.49
|
||||
Output | 3.5763e-05 | 4.065e-05 | 5.2452e-05 | 0.0 | 0.00
|
||||
Modify | 0.05831 | 0.068811 | 0.077666 | 2.9 | 0.28
|
||||
Other | | 0.0292 | | | 0.12
|
||||
|
||||
Nlocal: 78.75 ave 96 max 65 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1233 ave 1348 max 1116 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 9467.25 ave 12150 max 7160 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 37869
|
||||
Ave neighs/atom = 120.219
|
||||
Neighbor list builds = 37
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:24
|
||||
Reference in New Issue
Block a user