156 lines
5.6 KiB
Groff
156 lines
5.6 KiB
Groff
LAMMPS (8 Feb 2023)
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# QMMM with PySCF - mixture example
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units real
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atom_style full
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pair_style lj/cut/coul/long 12
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pair_modify mix arithmetic
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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kspace_style pppm 1e-5
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read_data data.mixture
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Reading data file ...
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orthogonal box = (0 0 0) to (31.351877 31.351877 31.351877)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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3081 atoms
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reading velocities ...
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3081 velocities
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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reading bonds ...
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2055 bonds
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reading angles ...
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1033 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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4 = max # of 1-2 neighbors
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3 = max # of 1-3 neighbors
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3 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.011 seconds
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# QM atoms are IDs 1 to 9
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# MM atoms are remaining atoms
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group qm id 1:9
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9 atoms in group qm
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group mm subtract all qm
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3072 atoms in group mm
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# remove bonds/angles between QM atoms
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# set charges to zero on QM atoms
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delete_bonds qm multi remove special
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System init for delete_bonds ...
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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G vector (1/distance) = 0.25751777
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grid = 24 24 24
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0020473396
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estimated relative force accuracy = 6.1655023e-06
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using double precision KISS FFT
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3d grid and FFT values/proc = 29791 13824
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Generated 21 of 21 mixed pair_coeff terms from arithmetic mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Deleting bonds ...
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2048 total bonds, 2048 turned on, 0 turned off
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1024 total angles, 1024 turned on, 0 turned off
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0 total dihedrals, 0 turned on, 0 turned off
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0 total impropers, 0 turned on, 0 turned off
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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set group qm charge 0.0
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Setting atom values ...
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9 settings made for charge
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neighbor 2.0 bin
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neigh_modify delay 0 every 1 check yes
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# QMMM dynamics
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timestep 0.01
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fix 1 all nve
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fix 2 qm mdi/qmmm direct elements N H C H Cl O H
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fix_modify 2 energy yes
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thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press
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thermo 1
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run 2
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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G vector (1/distance) = 0.25751777
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grid = 24 24 24
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0020473396
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estimated relative force accuracy = 6.1655023e-06
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using double precision KISS FFT
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3d grid and FFT values/proc = 29791 13824
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Generated 21 of 21 mixed pair_coeff terms from arithmetic mixing rule
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Per MPI rank memory allocation (min/avg/max) = 26.88 | 26.88 | 26.88 Mbytes
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Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
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0 0 0 0 103310.44 35284.412 88790.313 863.33521 -49804.536 -349295.05 -259641.4 -259641.4 897319.08
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1 15.497825 631.94375 5801.8092 97293.123 35284.413 82773 863.33444 -49804.536 -349294.57 -265658.24 -259856.43 852336.04
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2 31.725355 2211.4634 20303.213 82388.368 35284.413 67868.246 863.33213 -49804.536 -349292.7 -280561.12 -260257.91 741101.53
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Loop time of 31.7254 on 1 procs for 2 steps with 3081 atoms
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Performance: 0.000 ns/day, 440630.293 hours/ns, 0.063 timesteps/s, 194.229 atom-step/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.046066 | 0.046066 | 0.046066 | 0.0 | 0.15
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Bond | 0.00013947 | 0.00013947 | 0.00013947 | 0.0 | 0.00
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Kspace | 0.0040439 | 0.0040439 | 0.0040439 | 0.0 | 0.01
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00015604 | 0.00015604 | 0.00015604 | 0.0 | 0.00
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Output | 9.2355e-05 | 9.2355e-05 | 9.2355e-05 | 0.0 | 0.00
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Modify | 31.675 | 31.675 | 31.675 | 0.0 | 99.84
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Other | | 8.314e-05 | | | 0.00
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Nlocal: 3081 ave 3081 max 3081 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 17741 ave 17741 max 17741 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.77144e+06 ave 1.77144e+06 max 1.77144e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1771437
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Ave neighs/atom = 574.95521
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Ave special neighs/atom = 1.9941577
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:50
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