147 lines
6.0 KiB
Groff
147 lines
6.0 KiB
Groff
LAMMPS (23 Jun 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# water dimer with AMOEBA or HIPPO
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units real
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boundary s s s
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atom_style amoeba
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bond_style class2
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angle_style amoeba
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dihedral_style none
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# per-atom properties required by AMOEBA or HIPPO
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fix amtype all property/atom i_amtype ghost yes
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fix extra all property/atom i_amgroup d_redID d_pval ghost yes
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fix extra2 all property/atom i_polaxe d2_xyzaxis 3
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# read data file
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read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
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Reading data file ...
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orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
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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 = 0.003 seconds
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# force field
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pair_style amoeba
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pair_coeff * * amoeba_water.prm amoeba_water.key
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special_bonds lj/coul 0.5 0.5 0.5 one/five yes
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.5 0.5 0.5
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special bond factors coul: 0.5 0.5 0.5
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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 1-5 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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# thermo output
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compute virial all pressure NULL virial
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thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
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#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
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#dump_modify 1 sort id
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# zero step run
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#run 0
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# dynamics
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fix 1 all nve
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thermo 1
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run 5
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AMOEBA force field settings
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hal: cut 10 taper 8 vscale 0 0 1 1
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multipole: cut 10 aewald 0 mscale 0 0 0.4 1
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polar: cut 10 aewald 0
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pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
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precondition: cut 4.5
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Generated 0 of 1 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 = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 1 1 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair amoeba, 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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WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
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AMOEBA group count: 2
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Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes
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Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
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0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
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1 3.4764991 -5.1500622 0.021865831 0.65347737 0 0 0.67534321 -4.4229051 -8987.9108 -37684.452 39410.243 -29356.236 -80.130511 -27322.706 -69.79235
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2 12.286735 -5.1147506 0.014370337 0.49051077 0 0 0.50488111 -4.4267474 -865.99299 -23430.467 38420.372 -19944.197 -66.155435 -24835.896 -60.583907
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3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354
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4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932
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5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205
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Loop time of 0.000286908 on 1 procs for 5 steps with 6 atoms
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Performance: 1505.709 ns/day, 0.016 hours/ns, 17427.189 timesteps/s
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98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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AMOEBA timing breakdown:
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Init time: 7.417e-06 4.75%
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Hal time: 8.458e-06 5.42%
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Mpole time: 2.2734e-05 14.57%
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Induce time: 7.4016e-05 47.43%
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Polar time: 4.2972e-05 27.54%
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Total time: 0.00015604
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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 | 0.00015922 | 0.00015922 | 0.00015922 | 0.0 | 55.49
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Bond | 5.034e-06 | 5.034e-06 | 5.034e-06 | 0.0 | 1.75
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 8.49e-07 | 8.49e-07 | 8.49e-07 | 0.0 | 0.30
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Output | 0.00011336 | 0.00011336 | 0.00011336 | 0.0 | 39.51
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Modify | 2.093e-06 | 2.093e-06 | 2.093e-06 | 0.0 | 0.73
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Other | | 6.355e-06 | | | 2.21
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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: 0 ave 0 max 0 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 = 2
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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