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