126 lines
7.7 KiB
Groff
126 lines
7.7 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 simple weak electrolyte
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units lj
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atom_style charge
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neighbor 3.0 bin
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read_data data.chreg-acid
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Reading data file ...
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orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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219 atoms
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read_data CPU = 0.003 seconds
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variable cut_long equal 12.5
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variable nevery equal 100
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variable nmc equal 100
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variable pH equal 7.0
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variable pKa equal 6.0
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variable pIm equal 3.0
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variable pIp equal 3.0
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variable cut_lj equal 2^(1.0/6.0)
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variable lunit_nm equal 0.72 # in the units of nm
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velocity all create 1.0 8008 loop geom
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pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
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pair_style lj/cut/coul/long 1.12246204830937 ${cut_long}
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pair_style lj/cut/coul/long 1.12246204830937 12.5
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pair_coeff * * 1.0 1.0
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kspace_style ewald 1.0e-3
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pair_modify shift yes
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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 chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
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fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
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fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
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fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
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fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
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fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
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fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
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fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT
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thermo 100
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thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
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timestep 0.005
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run 2000
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Ewald 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) = 0.14221027
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estimated absolute RMS force accuracy = 0.0010128126
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estimated relative force accuracy = 0.0010128126
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KSpace vectors: actual max1d max3d = 257 5 665
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kxmax kymax kzmax = 5 5 5
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0 atoms in group FixChargeRegulation:exclusion_group:chareg
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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 = 15.5
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ghost atom cutoff = 15.5
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binsize = 7.75, bins = 7 7 7
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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/atomonly/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) = 11.89 | 11.89 | 11.89 Mbytes
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Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
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0 -0.049662059 1 0 0 1 99 0 0 109 10
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100 -0.06196414 1.0156327 100 72 15 85 0 0 93 8
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200 -0.053901683 0.95128403 200 160 24 76 0 0 87 11
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300 -0.043852423 0.98035058 300 246 22 78 0 0 85 7
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400 -0.048370798 1.0909844 400 324 16 84 0 0 91 7
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500 -0.042546472 1.026849 500 410 13 87 0 0 95 8
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600 -0.06133022 0.97805065 600 494 14 86 0 0 93 7
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700 -0.053815853 1.0641005 700 572 17 83 0 0 91 8
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800 -0.059974814 1.0192348 800 650 23 77 0 0 83 6
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900 -0.051808132 1.0773288 900 728 25 75 0 0 85 10
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1000 -0.050390995 1.0236954 1000 804 28 72 0 0 81 9
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1100 -0.069766444 1.030965 1100 890 25 75 0 0 85 10
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1200 -0.074580231 1.0490058 1200 963 21 79 0 0 88 9
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1300 -0.060169443 0.93456607 1300 1043 22 78 0 0 86 8
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1400 -0.05120764 1.0374062 1400 1127 19 81 0 0 92 11
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1500 -0.027644416 0.99804782 1500 1204 24 76 0 0 85 9
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1600 -0.038599195 0.99015524 1600 1283 22 78 0 0 90 12
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1700 -0.050222686 1.1444379 1700 1365 27 73 0 0 84 11
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1800 -0.049338003 1.1188048 1800 1449 22 78 0 0 84 6
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1900 -0.04533154 0.99894341 1900 1527 22 78 0 0 86 8
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2000 -0.058837311 0.95302017 2000 1608 26 74 0 0 81 7
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Loop time of 3.98119 on 4 procs for 2000 steps with 188 atoms
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Performance: 217020.495 tau/day, 502.362 timesteps/s
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96.2% 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 | 0.050626 | 0.061127 | 0.071318 | 3.4 | 1.54
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Kspace | 1.1987 | 1.2504 | 1.288 | 3.1 | 31.41
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Neigh | 0.0056982 | 0.0063858 | 0.0069821 | 0.7 | 0.16
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Comm | 0.068302 | 0.11638 | 0.17922 | 12.8 | 2.92
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Output | 0.00055408 | 0.00092399 | 0.0020106 | 0.0 | 0.02
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Modify | 2.5399 | 2.5406 | 2.5417 | 0.0 | 63.81
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Other | | 0.005394 | | | 0.14
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Nlocal: 47.0000 ave 55 max 42 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Nghost: 328.250 ave 335 max 317 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Neighs: 547.000 ave 659 max 466 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Total # of neighbors = 2188
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Ave neighs/atom = 11.638298
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Neighbor list builds = 2057
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Dangerous builds = 0
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Total wall time: 0:00:04
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