152 lines
6.3 KiB
Groff
152 lines
6.3 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.hippo 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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2 by 1 by 2 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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# force field
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pair_style hippo
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pair_coeff * * hippo_water.prm hippo_water.key
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Reading potential file hippo_water.prm with DATE: 2022-07-05
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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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HIPPO force field settings
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repulsion: cut 10 taper 8 rscale 0 0 1 1
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qxfer: cut 10 taper 8 mscale 0 0 0.4 1
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dispersion: cut 10 aewald 0 dspscale 0 0 0.4 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 0.2 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 hippo, 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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HIPPO group count: 2
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Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 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 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
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1 2.8239917 -5.0023563 0.021919009 0.46718 0 0 0.48909901 -4.4711684 -8777.4654 -33285.75 30332.24 -23920.463 -67.159404 -23940.605 -56.913519
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2 9.9359188 -4.9806071 0.014704278 0.34344685 0 0 0.35815113 -4.4743705 -1094.2989 -20777.766 32507.918 -16918.53 -57.217298 -21702.479 -51.827962
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3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978
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4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156
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5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154
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Loop time of 0.000488464 on 4 procs for 5 steps with 6 atoms
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Performance: 884.405 ns/day, 0.027 hours/ns, 10236.169 timesteps/s
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70.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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HIPPO timing breakdown:
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Init time: 1.2924e-05 4.50%
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Repulse time: 2.01283e-05 7.01%
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Disp time: 3.04475e-06 1.06%
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Mpole time: 3.51807e-05 12.25%
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Induce time: 0.000183034 63.71%
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Polar time: 3.13832e-05 10.92%
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Qxfer time: 1.44475e-06 0.50%
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Total time: 0.000287298
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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 | 0.00028193 | 0.00030553 | 0.00032173 | 0.0 | 62.55
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Bond | 1.317e-06 | 2.7712e-06 | 4.847e-06 | 0.0 | 0.57
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.3015e-05 | 3.0698e-05 | 4.1342e-05 | 0.0 | 6.28
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Output | 0.00012315 | 0.00013964 | 0.00015356 | 0.0 | 28.59
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Modify | 1.445e-06 | 1.881e-06 | 2.366e-06 | 0.0 | 0.39
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Other | | 7.949e-06 | | | 1.63
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Nlocal: 1.5 ave 3 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 4.5 ave 6 max 3 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 3.75 ave 12 max 0 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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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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