LAMMPS (8 Feb 2023) # QMMM with PySCF - two water 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.water 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 ... 6 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 4 bonds reading angles ... 2 angles 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 2 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.002 seconds # QM atoms are 1st water # MM atoms are 2nd water group qm molecule 1 3 atoms in group qm group mm molecule 2 3 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) = 0.21131887 grid = 12 12 12 stencil order = 5 estimated absolute RMS force accuracy = 0.0020500128 estimated relative force accuracy = 6.1735526e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4913 1728 Generated 1 of 1 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 ... 2 total bonds, 2 turned on, 0 turned off 1 total angles, 1 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 2 = max # of special neighbors special bonds CPU = 0.000 seconds set group qm charge 0.0 Setting atom values ... 3 settings made for charge neighbor 2.0 bin neigh_modify delay 0 every 1 check yes velocity all create 300.0 87287 loop geom # QMMM dynamics timestep 2.0 fix 1 all nve fix 2 qm mdi/qmmm direct elements 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 10 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.19767375 grid = 10 10 10 stencil order = 5 estimated absolute RMS force accuracy = 0.0022851662 estimated relative force accuracy = 6.8817102e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3375 1000 Generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule Per MPI rank memory allocation (min/avg/max) = 7.165 | 7.165 | 7.165 Mbytes Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press 0 0 300 4.4712151 -0.001256507 37.096223 -0.0091688448 0.95028479 -37.104135 -47941.423 -47940.482 -47936.011 -5.0247548 1 1.1968804 513.16171 7.648188 -0.0012517531 37.10766 -0.0088283103 1.3202413 -37.115237 -47947.2 -47945.888 -47938.24 -15.573297 2 1.9724248 476.87504 7.1073695 -0.0012428971 37.140547 -0.0078675595 0.14078812 -37.147172 -47942.073 -47941.94 -47934.833 14.589499 3 2.7513453 552.16501 8.229495 -0.0012247602 37.169663 -0.0070877422 0.97249224 -37.175526 -47943.52 -47942.554 -47934.325 32.307141 4 3.5346497 311.7073 4.6457012 -0.001214705 37.181636 -0.0067643983 0.92481745 -37.187186 -47938.682 -47937.764 -47933.119 0.56843394 5 4.3365751 545.29533 8.127109 -0.0012142012 37.183759 -0.0065649511 1.9626978 -37.18911 -47947.023 -47945.067 -47936.939 -16.524321 6 5.2102345 471.76402 7.0311947 -0.0012147223 37.184705 -0.0063050524 1.0470598 -37.189795 -47935.826 -47934.786 -47927.754 6.8723453 7 6.0808829 920.71341 13.722359 -0.0012039124 37.17538 -0.0062927565 1.1513661 -37.180469 -47936.811 -47935.666 -47921.944 41.323731 8 6.9043177 371.4235 5.5357146 -0.0012015277 37.147481 -0.0067304894 0.30070096 -37.15301 -47926.094 -47925.8 -47920.265 9.8713378 9 7.8167252 1313.1205 19.570814 -0.0012060836 37.113576 -0.0073073482 0.92112803 -37.119677 -47946.778 -47945.865 -47926.294 0.79522299 10 8.6886512 1925.2824 28.694506 -0.0012122896 37.098911 -0.0073851866 1.0565498 -37.105084 -47893.125 -47892.076 -47863.381 31.561426 Loop time of 8.68868 on 1 procs for 10 steps with 6 atoms Performance: 0.199 ns/day, 120.676 hours/ns, 1.151 timesteps/s, 6.906 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 | 3.9169e-05 | 3.9169e-05 | 3.9169e-05 | 0.0 | 0.00 Bond | 2.4067e-05 | 2.4067e-05 | 2.4067e-05 | 0.0 | 0.00 Kspace | 0.0012065 | 0.0012065 | 0.0012065 | 0.0 | 0.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 1.4026e-05 | 1.4026e-05 | 1.4026e-05 | 0.0 | 0.00 Output | 0.00026063 | 0.00026063 | 0.00026063 | 0.0 | 0.00 Modify | 8.6871 | 8.6871 | 8.6871 | 0.0 | 99.98 Other | | 2.512e-05 | | | 0.00 Nlocal: 6 ave 6 max 6 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 42 ave 42 max 42 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15 ave 15 max 15 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15 Ave neighs/atom = 2.5 Ave special neighs/atom = 1 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:09