235 lines
11 KiB
Plaintext
235 lines
11 KiB
Plaintext
LAMMPS (4 May 2022)
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# QMMM for SiO2 zeolite with one methane molecule
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units metal
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atom_style full
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bond_style harmonic
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angle_style harmonic
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read_data data.zeolite
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Reading data file ...
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orthogonal box = (-5.9266 -5.9266 -5.9266) to (5.9926 5.9926 5.9926)
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2 by 4 by 4 MPI processor grid
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reading atoms ...
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77 atoms
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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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4 bonds
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reading angles ...
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6 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 = 0.002 seconds
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read_data CPU = 0.021 seconds
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group mm type 1 2
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72 atoms in group mm
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group qm type 3 4
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5 atoms in group qm
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# pair style must define stand-alone short-range Coulombics
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# must specify mixing explicitly b/c hybrid/overlay
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# MM Si,O = types 1,2
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# QM C,H = types 3,4
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# MM Si,O atoms do not LJ interact with each other (just via Buckingham)
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# QM C,H atoms do not LJ interact with each other
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# MM Si,O and QM C,H do LJ interact with each other
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pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
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pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
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pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
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pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
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pair_coeff 1 3 lj/cut 0.009087 3.613
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pair_coeff 1 4 lj/cut 0.00344258 3.238
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pair_coeff 2 3 lj/cut 0.01419429 3.1
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pair_coeff 2 4 lj/cut 0.0035857762359063315 1.932779 # same as water dimer
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pair_coeff 3 3 lj/cut 0.0 3.4
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pair_coeff 4 4 lj/cut 0.0 2.65
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pair_coeff * * coul/cut
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bond_style harmonic
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bond_coeff 1 29.40 1.09
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angle_style harmonic
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angle_coeff 1 0.172325 109.5
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# remove bonds/angles in QM methane molecule
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delete_bonds qm multi remove special
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System init for delete_bonds ...
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 8.5
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ghost atom cutoff = 8.5
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binsize = 4.25, bins = 3 3 3
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair buck, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair lj/cut, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) pair coul/cut, 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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0 total bonds, 0 turned on, 0 turned off
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0 total angles, 0 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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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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velocity all create 300.0 458732
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neighbor 1.0 bin
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neigh_modify delay 0 every 1 check yes
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# dynamic or frozen zeolite
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#fix 1 all nve
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fix 1 qm nve
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fix 2 qm nwchem template.methane.nw methane.nw log.pwdft.zeolite Si O C H
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fix_modify 2 energy yes
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# convert dump file forces to Hartree/Bohr for comparison to NWChem
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variable fx atom fx/1185.8
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variable fy atom fy/1185.8
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variable fz atom fz/1185.8
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dump 1 all custom 1 dump.zeolite.qmmm id x y z q v_fx v_fy v_fz
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dump_modify 1 sort id format float "%20.16g"
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# small timestep for QMMM
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timestep 0.0001
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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 20
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Calling pspw_input() in NWChem ...
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time = 4.968 seconds
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Calling pspw_qmmm() in NWChem ...
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time = 6.503 seconds
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Per MPI rank memory allocation (min/avg/max) = 11.26 | 11.26 | 11.26 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 2.9471313 -102.3998 -1065.0369 -1167.4367 0 0 -198.9818 -1366.4185 -1363.4714 5517.5432
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Calling pspw_qmmm() in NWChem ...
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time = 3.868 seconds
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1 3.8686158 299.95086 2.9466486 -102.39975 -1065.1059 -1167.5057 0 0 -198.90989 -1366.4156 -1363.4689 5495.4255
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Calling pspw_qmmm() in NWChem ...
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time = 3.839 seconds
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2 7.7086679 299.89221 2.9460724 -102.39971 -1065.1824 -1167.5821 0 0 -198.83094 -1366.413 -1363.4669 5470.9047
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Calling pspw_qmmm() in NWChem ...
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time = 3.828 seconds
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3 11.53711 299.8247 2.9454092 -102.39967 -1065.2698 -1167.6695 0 0 -198.74163 -1366.4111 -1363.4657 5442.8579
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Calling pspw_qmmm() in NWChem ...
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time = 3.874 seconds
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4 15.411604 299.74946 2.94467 -102.39963 -1065.3685 -1167.7681 0 0 -198.64174 -1366.4099 -1363.4652 5411.2193
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Calling pspw_qmmm() in NWChem ...
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time = 3.867 seconds
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5 19.279369 299.66809 2.9438707 -102.39959 -1065.4787 -1167.8782 0 0 -198.53108 -1366.4093 -1363.4655 5375.9224
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Calling pspw_qmmm() in NWChem ...
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time = 3.884 seconds
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6 23.164177 299.58269 2.9430317 -102.39955 -1065.6006 -1168.0001 0 0 -198.4094 -1366.4095 -1363.4665 5336.8881
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Calling pspw_qmmm() in NWChem ...
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time = 3.931 seconds
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7 27.095936 299.49578 2.9421779 -102.39951 -1065.7347 -1168.1342 0 0 -198.27641 -1366.4106 -1363.4684 5294.0245
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Calling pspw_qmmm() in NWChem ...
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time = 3.995 seconds
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8 31.091727 299.41036 2.9413388 -102.39947 -1065.8812 -1168.2807 0 0 -198.13177 -1366.4125 -1363.4711 5247.225
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Calling pspw_qmmm() in NWChem ...
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time = 3.917 seconds
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9 35.008957 299.32983 2.9405477 -102.39943 -1066.0408 -1168.4402 0 0 -197.9751 -1366.4153 -1363.4748 5196.3675
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Calling pspw_qmmm() in NWChem ...
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time = 3.938 seconds
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10 38.948036 299.25799 2.9398419 -102.39939 -1066.2138 -1168.6132 0 0 -197.80594 -1366.4191 -1363.4793 5141.3097
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Calling pspw_qmmm() in NWChem ...
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time = 5.938 seconds
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11 44.886417 300.13711 2.9484783 -102.3987 -1112.1634 -1214.5621 0 0 -163.28337 -1377.8455 -1374.897 -9344.0882
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Calling pspw_qmmm() in NWChem ...
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time = 4.213 seconds
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12 49.100354 302.20838 2.9688259 -102.39866 -1113.0737 -1215.4724 0 0 -162.44687 -1377.9192 -1374.9504 -9618.386
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Calling pspw_qmmm() in NWChem ...
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time = 4.522 seconds
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13 53.622594 304.73496 2.9936465 -102.39862 -1114.1542 -1216.5529 0 0 -161.45551 -1378.0084 -1375.0147 -9943.5638
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Calling pspw_qmmm() in NWChem ...
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time = 4.301 seconds
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14 57.924103 307.82384 3.0239909 -102.39858 -1115.4521 -1217.8506 0 0 -160.26631 -1378.1169 -1375.093 -10333.782
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Calling pspw_qmmm() in NWChem ...
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time = 4.587 seconds
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15 62.511538 311.60627 3.0611487 -102.39853 -1117.0209 -1219.4194 0 0 -158.83006 -1378.2495 -1375.1883 -10805.182
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Calling pspw_qmmm() in NWChem ...
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time = 6.373 seconds
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16 68.884983 321.46762 3.1580243 -102.39783 -1190.4155 -1292.8133 0 0 -103.41532 -1396.2286 -1393.0706 -33890.787
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Calling pspw_qmmm() in NWChem ...
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time = 7.227 seconds
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17 76.112329 354.58063 3.4833189 -102.39711 -1297.586 -1399.9831 0 0 -21.400411 -1421.3835 -1417.9002 -67484.92
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Calling pspw_qmmm() in NWChem ...
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time = 5.903 seconds
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18 82.015607 426.41585 4.1890116 -102.39703 -1319.896 -1422.293 0 0 -1.3910438 -1423.6841 -1419.4951 -74076.209
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Calling pspw_qmmm() in NWChem ...
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time = 6.612 seconds
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19 88.628069 543.11841 5.3354708 -102.39692 -1357.8053 -1460.2022 0 0 32.790891 -1427.4114 -1422.0759 -85309.358
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Calling pspw_qmmm() in NWChem ...
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time = 7.909 seconds
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20 96.537191 722.72131 7.0998486 -102.39678 -1420.4861 -1522.8829 0 0 89.745396 -1433.1375 -1426.0376 -103965.42
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Loop time of 96.5372 on 32 procs for 20 steps with 77 atoms
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Performance: 0.002 ns/day, 13407.950 hours/ns, 0.207 timesteps/s
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99.8% CPU use with 32 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 | 0.00030032 | 0.00063124 | 0.00098374 | 0.0 | 0.00
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Bond | 4.4281e-05 | 7.7957e-05 | 0.00012963 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0016224 | 0.0018103 | 0.0021141 | 0.3 | 0.00
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Output | 0.0050295 | 0.0052005 | 0.0057519 | 0.2 | 0.01
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Modify | 96.528 | 96.528 | 96.529 | 0.0 | 99.99
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Other | | 0.001124 | | | 0.00
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Nlocal: 2.40625 ave 7 max 0 min
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Histogram: 4 10 3 0 6 6 0 0 2 1
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Nghost: 313.344 ave 405 max 225 min
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Histogram: 7 1 0 0 12 4 0 0 0 8
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Neighs: 98.3125 ave 324 max 0 min
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Histogram: 5 10 2 5 5 2 0 0 2 1
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Total # of neighbors = 3146
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Ave neighs/atom = 40.857143
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:01:48
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