forked from lijiext/lammps
140 lines
5.9 KiB
Groff
140 lines
5.9 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
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using 1 OpenMP thread(s) per MPI task
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units real
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dimension 3
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boundary p p p
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atom_style full
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pair_style lj/cut/coul/long 10.0
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bond_style harmonic
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angle_style harmonic
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read_data data.spce
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Reading data file ...
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orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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8640 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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5760 bonds
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reading angles ...
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2880 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 = 0.002 seconds
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read_data CPU = 0.048 seconds
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molecule h2omol H2O.txt
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Read molecule template h2omol:
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1 molecules
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0 fragments
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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### Flexible SPC/E Potential Parameters ###
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### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
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pair_coeff 1 1 0.1502629 3.1169
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pair_coeff 1 2 0.0341116368 2.04845
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pair_coeff 2 2 0.00774378 0.98
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bond_coeff 1 176.864 0.9611
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angle_coeff 1 42.1845 109.4712
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kspace_style pppm 1.0e-4
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fix mywidom all widom 10 20 0 29494 298 mol h2omol
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fix 2 all nvt temp 298.0 298.0 100.0
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neighbor 2.0 bin
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neigh_modify delay 10 every 2 check yes
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#run variables
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timestep 0.5
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thermo 10
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thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.2690183
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grid = 24 24 24
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stencil order = 5
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estimated absolute RMS force accuracy = 0.024843102
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estimated relative force accuracy = 7.4814263e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 29791 13824
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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WARNING: Fix widom using full_energy option (src/MC/fix_widom.cpp:320)
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0 atoms in group FixWidom:widom_exclusion_group:mywidom
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0 atoms in group FixWidom:rotation_gas_atoms:mywidom
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:654)
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Neighbor list info ...
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update: every = 2 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 = 8 8 8
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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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Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes
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Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.0447118 0 0 82468.116
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10 -29718 -32598.944 111.87604 -498.88935 82468.116 1.0447118 200.15526 1.6274344e-147 82468.116
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20 -29698.227 -32625.357 113.6696 -3120.7115 82468.116 1.0447118 -1.0295764 5.6893637 82468.116
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30 -29668.463 -33188.922 136.71037 -8129.0179 82468.116 1.0447118 5.5971294 7.856256e-05 82468.116
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40 -29654.066 -34017.797 169.45726 -5730.6427 82468.116 1.0447118 128.14313 1.0550462e-94 82468.116
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50 -29627.714 -33214.549 139.28799 -3954.0179 82468.116 1.0447118 122.28545 2.0851209e-90 82468.116
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60 -29602.616 -32995.039 131.73836 -8099.2136 82468.116 1.0447118 -1.4752191 12.07497 82468.116
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70 -29591.096 -33872.451 166.25834 -7065.2821 82468.116 1.0447118 17.210054 2.3911575e-13 82468.116
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80 -29553.631 -32971.209 132.7152 -3535.4257 82468.116 1.0447118 11.148921 6.6631697e-09 82468.116
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90 -29530.109 -33346.146 148.18857 -5312.6414 82468.116 1.0447118 51.783293 1.055658e-38 82468.116
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100 -29505.327 -34074.801 177.4469 -5991.0034 82468.116 1.0447118 32.415523 1.6878187e-24 82468.116
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Loop time of 55.4401 on 1 procs for 100 steps with 8640 atoms
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Performance: 0.078 ns/day, 308.000 hours/ns, 1.804 timesteps/s, 15.584 katom-step/s
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99.8% CPU use with 1 MPI tasks x 1 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 | 5.4117 | 5.4117 | 5.4117 | 0.0 | 9.76
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Bond | 0.029451 | 0.029451 | 0.029451 | 0.0 | 0.05
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Kspace | 0.73758 | 0.73758 | 0.73758 | 0.0 | 1.33
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Neigh | 1.4296 | 1.4296 | 1.4296 | 0.0 | 2.58
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Comm | 0.018593 | 0.018593 | 0.018593 | 0.0 | 0.03
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Output | 0.00069303 | 0.00069303 | 0.00069303 | 0.0 | 0.00
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Modify | 47.81 | 47.81 | 47.81 | 0.0 | 86.24
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Other | | 0.002525 | | | 0.00
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Nlocal: 8640 ave 8640 max 8640 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 23534 ave 23534 max 23534 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3.27356e+06 ave 3.27356e+06 max 3.27356e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3273560
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Ave neighs/atom = 378.88426
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Ave special neighs/atom = 2
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Neighbor list builds = 220
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Dangerous builds = 0
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Total wall time: 0:00:55
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