281 lines
19 KiB
Groff
281 lines
19 KiB
Groff
LAMMPS (21 Nov 2023)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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## This 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
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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
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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
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Performance: 0.258 ns/day, 92.958 hours/ns, 11.953 timesteps/s, 14.941 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 | 31.016 | 31.016 | 31.016 | 0.0 | 74.15
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Neigh | 2.2849 | 2.2849 | 2.2849 | 0.0 | 5.46
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Comm | 0.020391 | 0.020391 | 0.020391 | 0.0 | 0.05
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Output | 0.0019403 | 0.0019403 | 0.0019403 | 0.0 | 0.00
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Modify | 8.505 | 8.505 | 8.505 | 0.0 | 20.33
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Other | | 0.003238 | | | 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: 8489 ave 8489 max 8489 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 606382 ave 606382 max 606382 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 606382
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Ave neighs/atom = 485.1056
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:01:23
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