132 lines
6.7 KiB
Groff
132 lines
6.7 KiB
Groff
LAMMPS (10 Feb 2021)
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using 1 OpenMP thread(s) per MPI task
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# Charge regulation lammps for a polymer chain
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units lj
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atom_style full
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neighbor 3.0 bin
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read_data data.chreg-polymer
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Reading data file ...
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orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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160 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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79 bonds
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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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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.016 seconds
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bond_style harmonic
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bond_coeff 1 100 1.122462 # K R0
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velocity all create 1.0 8008 loop geom
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pair_style lj/cut/coul/long 1.122462 20
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pair_coeff * * 1.0 1.0 1.122462 # charges
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kspace_style pppm 1.0e-3
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pair_modify shift yes
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dielectric 1.0
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######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
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fix fnve all nve
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compute dtemp all temp
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compute_modify dtemp dynamic yes
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fix fT all langevin 1.0 1.0 1.0 123
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fix_modify fT temp dtemp
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fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
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fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
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fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
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thermo 100
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# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
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thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
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timestep 0.005
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run 2000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
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G vector (1/distance) = 0.077106934
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grid = 8 8 8
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stencil order = 5
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estimated absolute RMS force accuracy = 0.00074388331
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estimated relative force accuracy = 0.00074388331
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using double precision FFTW3
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3d grid and FFT values/proc = 1053 128
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0 atoms in group FixChargeRegulation:exclusion_group:chareg1
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0 atoms in group FixChargeRegulation:exclusion_group:chareg2
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0 atoms in group FixChargeRegulation:exclusion_group:chareg3
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
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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 = 23
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ghost atom cutoff = 23
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binsize = 11.5, bins = 9 9 9
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.878 | 6.935 | 6.992 Mbytes
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Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
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0 0.50528297 1 0 80 80 0 0 0
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100 0.60223729 0.89547569 13 67 75 8 0 0
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200 0.65253636 0.87662399 18 62 78 16 0 0
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300 0.51550501 1.0542131 22 58 84 27 1 0
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400 0.43566766 0.94557633 26 54 90 36 0 0
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500 0.36269507 1.0386276 31 49 94 45 0 0
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600 0.32430641 0.99903033 27 53 111 58 0 0
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700 0.30255299 0.91225991 28 52 121 69 0 0
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800 0.27189951 0.9747089 28 52 127 75 0 0
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900 0.25495247 1.0747821 28 52 135 83 0 0
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1000 0.25950416 0.95256449 32 48 134 86 0 0
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1100 0.22561248 1.0102255 32 48 147 99 0 0
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1200 0.1734754 0.99475154 33 47 157 110 0 0
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1300 0.20081084 0.99873599 36 44 160 116 0 0
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1400 0.14240417 0.99442152 36 44 164 121 1 0
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1500 0.15314186 0.94559876 39 41 167 126 0 0
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1600 0.13574107 1.0484195 43 37 164 127 0 0
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1700 0.14477789 1.0105172 42 38 166 128 0 0
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1800 0.13493107 1.0349667 41 39 171 132 0 0
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1900 0.14849779 0.9994329 33 47 178 131 0 0
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2000 0.14485171 0.99739608 34 46 183 137 0 0
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Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms
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Performance: 270955.695 tau/day, 627.212 timesteps/s
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94.5% CPU use with 4 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 | 0.086456 | 0.11738 | 0.18562 | 11.8 | 3.68
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Bond | 0.00099182 | 0.0018544 | 0.0030079 | 1.8 | 0.06
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Kspace | 0.77406 | 0.79354 | 0.80895 | 1.5 | 24.89
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Neigh | 0.017894 | 0.017948 | 0.018002 | 0.0 | 0.56
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Comm | 0.029044 | 0.07885 | 0.11432 | 11.3 | 2.47
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Output | 0.00054932 | 0.0009656 | 0.0021319 | 0.0 | 0.03
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Modify | 2.1676 | 2.1706 | 2.1733 | 0.2 | 68.07
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Other | | 0.007591 | | | 0.24
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Nlocal: 100.000 ave 110 max 89 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 415.000 ave 418 max 411 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Neighs: 1360.75 ave 1872 max 1018 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Total # of neighbors = 5443
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Ave neighs/atom = 13.607500
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Ave special neighs/atom = 1.1700000
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Neighbor list builds = 1492
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Dangerous builds = 0
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Total wall time: 0:00:03
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