156 lines
5.5 KiB
Groff
156 lines
5.5 KiB
Groff
LAMMPS (22 Dec 2022)
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# QMMM with PySCF
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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.water
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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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6 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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4 bonds
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reading angles ...
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2 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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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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2 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.004 seconds
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# QM atoms are 1st water
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# MM atoms are 2nd water
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group qm molecule 1
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3 atoms in group qm
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group mm molecule 2
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3 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) = 0.21131887
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grid = 12 12 12
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0020500128
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estimated relative force accuracy = 6.1735526e-06
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using double precision KISS FFT
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3d grid and FFT values/proc = 4913 1728
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Generated 1 of 1 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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2 total bonds, 2 turned on, 0 turned off
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1 total angles, 1 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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2 = 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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3 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 2.0
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fix 1 all nve
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fix 2 qm mdi/qmmm direct elements 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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mdi plugin pyscf_mdi mdi "-role ENGINE -name PySCF -method LINK" extra "-pbc no" command "run 2"
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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) = 0.19767375
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grid = 10 10 10
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0022851662
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estimated relative force accuracy = 6.8817102e-06
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using double precision KISS FFT
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3d grid and FFT values/proc = 3375 1000
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Generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule
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Per MPI rank memory allocation (min/avg/max) = 7.165 | 7.165 | 7.165 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 -0.001256507 37.096223 -0.0091688448 0.95028479 -37.104135 -47941.423 -47940.482 -47940.482 -11.65711
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1 13.839254 274.73153 4.0946125 -0.001258094 37.106014 -0.0088915927 0.62503382 -37.113647 -47947.815 -47947.199 -47943.104 5.9530005
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2 28.396141 121.44569 1.8100327 -0.0012589509 37.125978 -0.0083996825 0.32331257 -37.133119 -47938.851 -47938.536 -47936.726 14.80352
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Loop time of 28.3962 on 1 procs for 2 steps with 6 atoms
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Performance: 0.012 ns/day, 1971.958 hours/ns, 0.070 timesteps/s, 0.423 atom-step/s
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747.8% 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 | 1.4093e-05 | 1.4093e-05 | 1.4093e-05 | 0.0 | 0.00
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Bond | 9.672e-06 | 9.672e-06 | 9.672e-06 | 0.0 | 0.00
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Kspace | 0.00032919 | 0.00032919 | 0.00032919 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 6.136e-06 | 6.136e-06 | 6.136e-06 | 0.0 | 0.00
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Output | 0.00012034 | 0.00012034 | 0.00012034 | 0.0 | 0.00
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Modify | 28.396 | 28.396 | 28.396 | 0.0 |100.00
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Other | | 1.567e-05 | | | 0.00
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Nlocal: 6 ave 6 max 6 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 42 ave 42 max 42 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 15 ave 15 max 15 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 15
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Ave neighs/atom = 2.5
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Ave special neighs/atom = 1
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:43
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