164 lines
7.0 KiB
Groff
164 lines
7.0 KiB
Groff
LAMMPS (8 Feb 2023)
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# QMMM with PySCF - two water 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.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 = 0.002 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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velocity all create 300.0 87287 loop geom
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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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run 10
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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 0 300 4.4712151 -0.001256507 37.096223 -0.0091688448 0.95028479 -37.104135 -47941.423 -47940.482 -47936.011 -5.0247548
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Loop time of 8.68868 on 1 procs for 10 steps with 6 atoms
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Performance: 0.199 ns/day, 120.676 hours/ns, 1.151 timesteps/s, 6.906 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 | 3.9169e-05 | 3.9169e-05 | 3.9169e-05 | 0.0 | 0.00
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Bond | 2.4067e-05 | 2.4067e-05 | 2.4067e-05 | 0.0 | 0.00
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Kspace | 0.0012065 | 0.0012065 | 0.0012065 | 0.0 | 0.01
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.4026e-05 | 1.4026e-05 | 1.4026e-05 | 0.0 | 0.00
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Output | 0.00026063 | 0.00026063 | 0.00026063 | 0.0 | 0.00
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Modify | 8.6871 | 8.6871 | 8.6871 | 0.0 | 99.98
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Other | | 2.512e-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: 0:00:09
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